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Bibliography on: Symbiosis

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 20 Jul 2024 at 01:56 Created: 

Symbiosis

Symbiosis refers to an interaction between two or more different organisms living in close physical association, typically to the advantage of both. Symbiotic relationships were once thought to be exceptional situations. Recent studies, however, have shown that every multicellular eukaryote exists in a tight symbiotic relationship with billions of microbes. The associated microbial ecosystems are referred to as microbiome and the combination of a multicellular organism and its microbiota has been described as a holobiont. It seems "we are all lichens now."

Created with PubMed® Query: ( symbiosis[tiab] OR symbiotic[tiab] ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2024-07-19

Idowu AP, Yamamoto K, Koizumi T, et al (2024)

Changes in the rhizosphere and root-associated bacteria community of white Guinea yam (Dioscorea rotundata Poir.) impacted by genotype and nitrogen fertilization.

Heliyon, 10(12):e33169.

The bacterial diversity and composition of water yam (Dioscorea alata L. cv. A-19), which can grow without chemical fertilization, have recently been characterized with no significant differences compared with the use of chemical fertilization. However, the diversity and community structure of bacteria associated with the white Guinea yam (Dioscorea rotundata), the most cultivated and economically important yam in West Africa, have not yet been investigated. This study characterized the bacterial diversity and composition associated with bulk soil, rhizosphere, and plant roots in six white Guinea yam genotypes (S004, S020, S032, S042, S058, and S074) in field experiments in Ibadan, Nigeria under N-based chemical fertilizer application. The largest diversity of bacteria was found in the bulk soil, followed by the rhizosphere and roots. Based on the alpha diversity analysis, the bacterial diversity in both S020 and S042 increased with fertilizer application among the bulk soil samples. S058 grown under no-fertilizer conditions had the highest bacterial diversity among the rhizosphere samples. Beta diversity analysis highlighted the significant difference in the composition of bacteria associated with the genotypes and fertilizer treatments, and S032 had a unique bacterial composition compared to the other genotypes. The dominant phylum across all sample types was Proteobacteria. Actinobacteriota was the dominant phylum among bulk soil samples. At the genus level, Bacillus was the most abundant bacterial genus across both the control and treated samples. Pseudomonas was predominant across all rhizosphere samples. Chryseobacterium, Sphingobium, Delftia and Klebsiella associated with the rhizosphere were shown the altered relative abundance between the control and treated samples depending on genotypes. A genus related to symbiotic nitrogen-fixing bacteria, the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, showed higher relative abundance among all root samples, indicating that it is a core bacterial genus. Furthermore, the field application of chemical fertilizer had a significant impact on the relative abundances of two genera related to symbiotic nitrogen-fixers, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade and Bradyrhizobium in the rhizosphere and root. These results suggest that N-based chemical fertilizers and plant genotypes would influence the compositional arrangement of associated bacterial communities, including symbiotic nitrogen-fixing bacteria.

RevDate: 2024-07-19

Aihetanmu S, Liang Z, Zhang X, et al (2024)

Genetic specialization of key bifidobacterial phylotypes in multiple mother-infant dyad cohorts from geographically isolated populations.

Frontiers in microbiology, 15:1399743.

Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. Bifidobacteria are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and in vitro carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to B. longum subsp. longum, B. breve, and B. animalis subsp. lactis, respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of Bifidobacterium phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that B. longum subsp. longum and B. breve exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of B. animalis subsp. lactis were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of Bifidobacterium species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications.

RevDate: 2024-07-19

Nakhforoosh A, Hallin E, Karunakaran C, et al (2024)

Visualization and Quantitative Evaluation of Functional Structures of Soybean Root Nodules via Synchrotron X-ray Imaging.

Plant phenomics (Washington, D.C.), 6:0203.

The efficiency of N2-fixation in legume-rhizobia symbiosis is a function of root nodule activity. Nodules consist of 2 functionally important tissues: (a) a central infected zone (CIZ), colonized by rhizobia bacteria, which serves as the site of N2-fixation, and (b) vascular bundles (VBs), serving as conduits for the transport of water, nutrients, and fixed nitrogen compounds between the nodules and plant. A quantitative evaluation of these tissues is essential to unravel their functional importance in N2-fixation. Employing synchrotron-based x-ray microcomputed tomography (SR-μCT) at submicron resolutions, we obtained high-quality tomograms of fresh soybean root nodules in a non-invasive manner. A semi-automated segmentation algorithm was employed to generate 3-dimensional (3D) models of the internal root nodule structure of the CIZ and VBs, and their volumes were quantified based on the reconstructed 3D structures. Furthermore, synchrotron x-ray fluorescence imaging revealed a distinctive localization of Fe within CIZ tissue and Zn within VBs, allowing for their visualization in 2 dimensions. This study represents a pioneer application of the SR-μCT technique for volumetric quantification of CIZ and VB tissues in fresh, intact soybean root nodules. The proposed methods enable the exploitation of root nodule's anatomical features as novel traits in breeding, aiming to enhance N2-fixation through improved root nodule activity.

RevDate: 2024-07-19

Li C, Han Y, Zou X, et al (2024)

A systematic discussion and comparison of the construction methods of synthetic microbial community.

Synthetic and systems biotechnology, 9(4):775-783.

Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.

RevDate: 2024-07-18

Shah I, Sarim KM, Sikka VK, et al (2024)

Developed Rhizobium Strains Enhance Soil Fertility and Yield of Legume Crops in Haryana, India.

Journal of basic microbiology [Epub ahead of print].

Three strains of Gram-negative bacterium, Rhizobium, were developed by gamma (γ)-irradiation random mutagenesis. The developed strains were evaluated for their augmented features for symbiotic association, nitrogen fixation, and crop yield of three leguminous plants-chickpea, field-pea, and lentil-in agricultural fields of the northern Indian state of Haryana. Crops treated with developed mutants exhibited significant improvement in plant features and the yield of crops when compared to the control-uninoculated crops and crops grown with indigenous or commercial crop-specific strains of Rhizobium. This improvement was attributed to generated mutants, MbPrRz1 (on chickpea), MbPrRz2 (on lentil), and MbPrRz3 (on field-pea). Additionally, the cocultured symbiotic response of MbPrRz1 and MbPrRz2 mutants was found to be more pronounced on all three crops. The statistical analysis using Pearson's correlation coefficients revealed that nodulation and plant biomass were the most related parameters of crop yield. Among the effectiveness of developed mutants, MbPrRz1 yielded the best results for all three tested crops. Moreover, the developed mutants enhanced macro- and micronutrients of the experimental fields when compared with fields harboring the indigenous rhizobial community. These developed mutants were further genetically characterized, predominantly expressing nitrogen fixation marker, nifH, and appeared to belong to Mesorhizobium ciceri (MbPrRz1) and Rhizobium leguminosarum (both MbPrRz2 and MbPrRz3). In summary, this study highlights the potential of developed Rhizobium mutants as effective biofertilizers for sustainable agriculture, showcasing their ability to enhance symbiotic relationships, crop yield, and soil fertility.

RevDate: 2024-07-18

Adhikari SK (2024)

Quasi-one- and quasi-two-dimensional symbiotic solitons bound by dipolar interaction.

Physical review. E, 109(6-1):064206.

We study the formation of quasi-one- (quasi-1D) and quasi-two-dimensional (quasi-2D) symbiotic solitons bound by an interspecies dipolar interaction in a binary dipolar Bose-Einstein condensate. These binary solitons have a repulsive intraspecies contact interaction stronger than the intraspecies dipolar interaction, so that they can not be bound in isolation in the absence of an interspecies dipolar interaction. These symbiotic solitons are bound in the presence of an interspecies dipolar interaction and zero interspecies contact interaction. The quasi-1D solitons are free to move along the polarization z direction of the dipolar atoms, whereas the quasi-2D solitons move in the x-z plane. To illustrate these, we consider a ^{164}Er-^{166}Er mixture with scattering lengths a(^{164}Er)=81a_{0} and a(^{166}Er)=68a_{0} and with dipolar lengths a_{dd}(^{164}Er)≈a_{dd}(^{166}Er)≈65a_{0}, where a_{0} is the Bohr radius. In each of the two components a>a_{dd}, which stops the binding of solitons in each component in isolation, whereas a binary quasi-1D or a quasi-2D ^{164}Er-^{166}Er soliton is bound in the presence of an interspecies dipolar interaction. The stationary states were obtained by imaginary-time propagation of the underlying mean-field model; dynamical stability of the solitons was established by real-time propagation over a long period of time.

RevDate: 2024-07-17
CmpDate: 2024-07-18

Fang CC, Liu YH, SH Huang (2024)

The symbiotic experiences of residents with and without dementia co-living in Taiwan's long-term care facilities: a phenomenological study.

BMC geriatrics, 24(1):611.

BACKGROUND: In Taiwan, residents with and without dementia mostly co-live in long-term care facilities. The behavioral and psychiatric symptoms of dementia residents often pose challenges for others living together. This study explored the symbiotic experiences of residents without dementia co-living with those with dementia in long-term care facilities in Taiwan to present their experiences of living together.

METHODS: This was a cross-sectional descriptive study with a phenomenological design. Semi-structured face-to-face interviews were conducted with 30 residents without dementia from three long-term care institutions in Taiwan. Colaizzi's data processing steps were used for analysis.

RESULTS: The analysis of interview transcripts revealed that the experiences of residents who lived with those with dementia were that of a "symbiosis." Three core themes were found: "the impact of co-living," "facing difficulties and coping," and "companionship and reciprocity." This study showed that residents without dementia may be affected by the behavioral and psychiatric symptoms of residents with dementia when co-living in long-term care facilities. However, there are also positive and mutually beneficial interactions between them. By helping people with dementia in their daily lives, residents without dementia feel happy and accomplished and their self-worth is enhanced. Furthermore, residents with dementia have more opportunities for social engagement and co-living interactions.

CONCLUSION: These results can guide long-term care facilities without special care dementia units to support residents without dementia, reduce the interference of the behavioral and psychiatric symptoms of residents with dementia, and promote mutual benefits. However, these findings warrant further investigation.

RevDate: 2024-07-17

Ren J, Cui Z, Wang Y, et al (2024)

Transcriptomic insights into the potential impacts of flavonoids and nodule-specific cysteine-rich peptides on nitrogen fixation in Vicia villosa and Vicia sativa.

Plant physiology and biochemistry : PPB, 214:108936 pii:S0981-9428(24)00604-1 [Epub ahead of print].

Vicia villosa (VV) and Vicia sativa (VS) are legume forages highly valued for their excellent nitrogen fixation. However, no research has addressed the mechanisms underlying their differences in nitrogen fixation. This study employed physiological, cytological, and comparative transcriptomic approaches to elucidate the disparities in nitrogen fixation between them. Our results showed that the total amount of nitrogen fixed was 60.45% greater in VV than in VS, and the comprehensive nitrogen response performance was 94.19% greater, while the nitrogen fixation efficiency was the same. The infection zone and differentiated bacteroid proportion in mature VV root nodules were 33.76% and 19.35% greater, respectively, than those in VS. The size of the VV genome was 15.16% larger than that of the VS genome, consistent with its greater biomass. A significant enrichment of the flavonoid biosynthetic pathway was found only for VV-specific genes, among which chalcone-flavonone isomerase, caffeoyl-CoA-O-methyltransferase and stilbene synthase were extremely highly expressed. The VV-specific genes also exhibited significant enrichment in symbiotic nodulation; genes related to nodule-specific cysteine-rich peptides (NCRs) comprised 61.11% of the highly expressed genes. qRT‒PCR demonstrated that greater enrichment and expression of the dominant NCR (Unigene0004451) were associated with greater nodule bacteroid differentiation and greater nitrogen fixation in VV. Our findings suggest that the greater total nitrogen fixation of VV was attributed to its larger biomass, leading to a greater nitrogen demand and enhanced fixation physiology. This process is likely achieved by the synergistic effects of high bacteroid differentiation along with high expression of flavonoid and NCR genes.

RevDate: 2024-07-17

Kho K, Cheng T, Buddelmeijer N, et al (2024)

When the Host Encounters the Cell Wall and Vice Versa.

Annual review of microbiology [Epub ahead of print].

Peptidoglycan (PGN) and associated surface structures such as secondary polymers and capsules have a central role in the physiology of bacteria. The exoskeletal PGN heteropolymer is the major determinant of cell shape and allows bacteria to withstand cytoplasmic turgor pressure. Thus, its assembly, expansion, and remodeling during cell growth and division need to be highly regulated to avoid compromising cell survival. Similarly, regulation of the assembly impacts bacterial cell shape; distinct shapes enhance fitness in different ecological niches, such as the host. Because bacterial cell wall components, in particular PGN, are exposed to the environment and unique to bacteria, these have been coopted during evolution by eukaryotes to detect bacteria. Furthermore, the essential role of the cell wall in bacterial survival has made PGN an important signaling molecule in the dialog between host and microbes and a target of many host responses. Millions of years of coevolution have resulted in a pivotal role for PGN fragments in shaping host physiology and in establishing a long-lasting symbiosis between microbes and the host. Thus, perturbations of this dialog can lead to pathologies such as chronic inflammatory diseases. Similarly, pathogens have devised sophisticated strategies to manipulate the system to enhance their survival and growth.

RevDate: 2024-07-17
CmpDate: 2024-07-17

Shoham S, Keren R, Lavy A, et al (2024)

Out of the blue: Hyperaccumulation of molybdenum in the Indo-Pacific sponge Theonella conica.

Science advances, 10(29):eadn3923.

Molybdenum is an essential micronutrient, but because of its toxicity at high concentrations, its accumulation in living organisms has not been widely demonstrated. In this study, we report that the marine sponge Theonella conica accumulates exceptionally high levels of molybdenum (46,793 micrograms per gram of dry weight) in a wide geographic distribution from the northern Red Sea to the reefs of Zanzibar, Indian Ocean. The element is found in various sponge body fractions and correlates to selenium. We further investigated the microbial composition of the sponge and compared it to its more studied congener, Theonella swinhoei. Our analysis illuminates the symbiotic bacterium Entotheonella sp. and its role in molybdenum accumulation. Through microscopic and analytical methods, we provide evidence of intracellular spheres within Entotheonella sp. that exhibit high molybdenum content, further unraveling the intricate mechanisms behind molybdenum accumulation in this sponge species and its significance in the broader context of molybdenum biogeochemical cycling.

RevDate: 2024-07-17
CmpDate: 2024-07-17

Scott TJ, Queller DC, JE Strassmann (2024)

Complex third-party effects in the Dictyostelium-Paraburkholderia symbiosis: prey bacteria that are eaten, carried or left behind.

Proceedings. Biological sciences, 291(2027):20241111.

Symbiotic interactions may change depending on third parties like predators or prey. Third-party interactions with prey bacteria are central to the symbiosis between Dictyostelium discoideum social amoeba hosts and Paraburkholderia bacterial symbionts. Symbiosis with inedible Paraburkholderia allows host D. discoideum to carry prey bacteria through the dispersal stage where hosts aggregate and develop into fruiting bodies that disperse spores. Carrying prey bacteria benefits hosts when prey are scarce but harms hosts when prey bacteria are plentiful, possibly because hosts leave some prey bacteria behind while carrying. Thus, understanding benefits and costs in this symbiosis requires measuring how many prey bacteria are eaten, carried and left behind by infected hosts. We found that Paraburkholderia infection makes hosts leave behind both symbionts and prey bacteria. However, the number of prey bacteria left uneaten was too small to explain why infected hosts produced fewer spores than uninfected hosts. Turning to carried bacteria, we found that hosts carry prey bacteria more often after developing in prey-poor environments than in prey-rich ones. This suggests that carriage is actively modified to ensure hosts have prey in the harshest conditions. Our results show that multi-faceted interactions with third parties shape the evolution of symbioses in complex ways.

RevDate: 2024-07-16

Duan S, Feng G, Limpens E, et al (2024)

Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum.

Nature reviews. Microbiology [Epub ahead of print].

The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF-plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant-AMF-bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF-bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture.

RevDate: 2024-07-16

Tewari N, P Dey (2024)

Navigating commensal dysbiosis: Gastrointestinal host-pathogen interplay orchestrating opportunistic infections.

Microbiological research, 286:127832 pii:S0944-5013(24)00233-7 [Epub ahead of print].

The gut commensals, which are usually symbiotic or non-harmful bacteria that live in the gastrointestinal tract, have a positive impact on the health of the host. This review, however, specifically discuss distinct conditions where commensals aid in the development of pathogenic opportunistic infections. We discuss that the categorization of gut bacteria as either pathogens or non-pathogens depends on certain circumstances, which are significantly affected by the tissue microenvironment and the dynamic host-microbe interaction. Under favorable circumstances, commensals have the ability to transform into opportunistic pathobionts by undergoing overgrowth. These conditions include changes in the host's physiology, simultaneous infection with other pathogens, effective utilization of nutrients, interactions between different species of bacteria, the formation of protective biofilms, genetic mutations that enhance pathogenicity, acquisition of genes associated with virulence, and the ability to avoid the host's immune response. These processes allow commensals to both initiate infections themselves and aid other pathogens in populating the host. This review highlights the need of having a detailed and sophisticated knowledge of the two-sided nature of gut commensals. Although commensals mostly promote health, they may also become harmful in certain changes in the environment or the body's functioning. This highlights the need of acknowledging the intricate equilibrium in interactions between hosts and microbes, which is crucial for preserving intestinal homeostasis and averting diseases. Finally, we also emphasize the further need of research to better understand and anticipate the behavior of gut commensals in different situations, since they play a crucial and varied role in human health and disease.

RevDate: 2024-07-16

Ni H, Hou X, Tian S, et al (2024)

Insights into the Early Steps of the Symbiotic Interaction between Soybean (Glycine max) and Sinorhizobium fredii Symbiosis Using Transcriptome, Small RNA, and Degradome Sequencing.

Journal of agricultural and food chemistry [Epub ahead of print].

Symbiotic nitrogen fixation carried out by the soybean-rhizobia symbiosis increases soybean yield and reduces the amount of nitrogen fertilizer that has been applied. MicroRNAs (miRNAs) are crucial in plant growth and development, prompting an investigation into their role in the symbiotic interaction of soybean with partner rhizobia. Through integrated small RNA, transcriptome, and degradome sequencing analysis, 1215 known miRNAs, 314 of them conserved, and 187 novel miRNAs were identified, with 44 differentially expressed miRNAs in soybean roots inoculated with Sinorhizobium fredii HH103 and a ttsI mutant. The study unveiled that the known miRNA gma-MIR398a-p5 was downregulated in the presence of the ttsI mutation, while the target gene of gma-MIR398a-p5, Glyma.06G007500, associated with nitrogen metabolism, was upregulated. The results of this study offer insights for breeding high-efficiency nitrogen-fixing soybean varieties, enhancing crop yield and quality.

RevDate: 2024-07-16

Drapek C, Rizza A, Mohd-Radzman NA, et al (2024)

GA dynamics governing nodulation revealed using GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula lateral organs.

The Plant cell pii:7714829 [Epub ahead of print].

During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determine the cellular location and function of bioactive GA during nodule organogenesis using a genetically-encoded second generation GA biosensor, GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula. We find endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions and maintaining accumulation in the mature nodule meristem. We show, through mis-expression of GA catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that nodule-identity genes induce and sustain GA accumulation necessary for proper nodule formation.

RevDate: 2024-07-16
CmpDate: 2024-07-16

Sgroi M, Hoey D, Medina Jimenez K, et al (2024)

The receptor-like kinase ARK controls symbiotic balance across land plants.

Proceedings of the National Academy of Sciences of the United States of America, 121(30):e2318982121.

The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.

RevDate: 2024-07-16
CmpDate: 2024-07-16

Zeb A, Khan Y, He H, et al (2024)

Molecular identification of Halomonas AZ07 and its multifunctional enzymatic activities to degrade Pyropia yezoensis under high-temperature condition.

Molecular biology reports, 51(1):816.

BACKGROUND: Pyropia yezoensis a commercially important red seaweed species, is susceptible to various microorganisms infections, among which bacterial infections are the most prominent ones. Pyropia yezoensis is often affected by harmful bacterial communities under high temperatures that can lead to its degradation and economic losses. The current study aimed to explore Pyropia yezoensis-associated microbiota and further identify potential isolates, which can degrade Pyropia yezoensis under high-temperature conditions.

METHODS AND RESULTS: The 16S rRNA gene sequencing was used to identify the agarolytic bacterial species. The results showed that Chromohalobacter sp. strain AZ6, Pseudoalteromonas sp. strain AZ, Psychrobacter sp. strain AZ3, Vibrio sp. strain AZ, and Halomonas sp. strain AZ07 exhibited algicidal properties as these strains were more abundant at high temperature (25 °C). Among the five isolated strains, the potential isolate Halomonas sp. strain AZ07 showed high production of agarolytic enzymes, including lipase, protease, cellulase, and amylase. This study confirmed that the isolated strain could produce these four different enzymes. The strain Halomonas AZ07 was co-treated with Pyropia yezoensis cells under two different temperature environments, including 13 °C and 25 °C. The degradation of Pyropia yezoensis occurred at the optimum temperature of 25 °C and effectively degraded their cell wall, proteins, lipids, and carbohydrates.

CONCLUSION: The successful cultivation of Pyropia yezoensis in coastal farm environments is dependent on specific temperature and environmental factors, and lower temperatures have been observed to be particularly beneficial for the survival and growth of Pyropia yezoensis. The temperature below 13 °C was confirmed to be the best niche for the symbiotic relationship of microbiota associated with Pyropia yezoensis for its growth, development, and production.

RevDate: 2024-07-16
CmpDate: 2024-07-16

Huang J, Xu J, Zhang H, et al (2024)

Combined Effects of Tetracycline and Copper Ion on Microorganisms During the Biological Phosphorus Removal.

Bulletin of environmental contamination and toxicology, 113(2):13.

Tetracycline and copper ion are common pollutants in wastewater, and the effects of mixed pollutants on microorganisms in wastewater biological treatment have been less studied. In order to reveal the effects of mixed pollutants of tetracycline and copper ion on the microorganisms during the biological phosphorus removal, three ratios of tetracycline and copper ions were designed by the direct equipartition ray method. The relative abundance and diversity of microbial community were investigated, and the microbial interactions were revealed through microbiological methods. The results demonstrated that, for three different ratios, the inhibitory effect of specific phosphorus uptake rate became more significant with the increase of the tetracycline-copper ions concentration and the reaction time. The microbial community decreased with the increase of the proportion of tetracycline in different ratios. The relative abundance of Acinetobacter decreased with the increase of the proportion of tetracycline, while the relative abundance of Ca.Competibacter was higher under the conditions of low mixtures concentrations. Positive interactions and symbiotic relationships among microorganisms were predominant for three different ratios. However, as the proportion of tetracycline increased, the community structure of microorganisms shifted from phosphate-accumulating organisms to glycogen accumulating organisms and denitrifying bacteria. This study can provide a reference for the effect of mixed pollutants on microorganisms and the mechanism of wastewater treatment.

RevDate: 2024-07-17

Del-Canto A, Sanz-Saez A, Heath KD, et al (2024)

Conventional management has a greater negative impact on Phaseolus vulgaris L. rhizobia diversity and abundance than water scarcity.

Frontiers in plant science, 15:1408125.

INTRODUCTION: Drought is one of the biggest problems for crop production and also affects the survival and persistence of soil rhizobia, which limits the establishment of efficient symbiosis and endangers the productivity of legumes, the main source of plant protein worldwide.

AIM: Since the biodiversity can be altered by several factors including abiotic stresses or cultural practices, the objective of this research was to evaluate the effect of water availability, plant genotype and agricultural management on the presence, nodulation capacity and genotypic diversity of rhizobia.

METHOD: A field experiment was conducted with twelve common bean genotypes under irrigation and rain-fed conditions, both in conventional and organic management. Estimation of the number of viable rhizobia present in soils was performed before the crop establishment, whereas the crop yield, nodule number and the strain diversity of bacteria present in nodules were determined at postharvest.

RESULTS: Rainfed conditions reduced the number of nodules and of isolated bacteria and their genetic diversity, although to a lesser extent than the agrochemical inputs related to conventional management. In addition, the effect of water scarcity on the conventional management soil was greater than observed under organic conditions.

CONCLUSIONS: The preservation of diversity will be a key factor to maintain crop production in the future, as problems caused by drought will be exacerbated by climate change and organic management can help to maintain the biodiversity of soil microbiota, a fundamental aspect for soil health and quality.

RevDate: 2024-07-17

Dagar J, Maurya S, Antil S, et al (2024)

Symbionts of Ciliates and Ciliates as Symbionts.

Indian journal of microbiology, 64(2):304-317.

Endosymbiotic relationships between ciliates and others are critical for their ecological roles, physiological adaptations, and evolutionary implications. These can be obligate and facultative. Symbionts often provide essential nutrients, contribute to the ciliate's metabolism, aid in digestion, and offer protection against predators or environmental stressors. In turn, ciliates provide a protected environment and resources for their symbionts, facilitating their survival and proliferation. Ultrastructural and full-cycle rRNA approaches are utilized to identify these endosymbionts. Fluorescence in situ hybridization using "species- and group-specific probes" which are complementary to the genetic material (DNA or RNA) of a particular species or group of interest represent convenient tools for their detection directly in the environment. A systematic survey of these endosymbionts has been conducted using both traditional and metagenomic approaches. Ciliophora and other protists have a wide range of prokaryotic symbionts, which may contain potentially pathogenic bacteria. Ciliates can establish symbiotic relationships with a variety of hosts also, ranging from protists to metazoans. Understanding ciliate symbiosis can provide useful insights into the complex relationships that drive microbial communities and ecosystems in general.

RevDate: 2024-07-17

Shinde DB, Mahore JG, Giram PS, et al (2024)

Microbiota of Saliva: A Non-invasive Diagnostic Tool.

Indian journal of microbiology, 64(2):328-342.

Potential of salivary microbiota as a non-invasive diagnostic tool for various diseases are explained in the present review. Traditional diagnostic methods rely on blood, which has limitations in terms of collection and biomarker specificity. We discuss the concept of normal flora and how disruptions in oral microbiota can be indicative of diseases. Saliva, harboring a diverse microbial community, offers promise as a diagnostic biomarker source for oral and non-oral conditions. We delve into the role of microbial dysbiosis in disease pathogenesis and the prospects of using biological indicators like dysbiosis for diagnosis, prediction, and monitoring. This review also emphasizes the significance of saliva microbiota in advancing early disease detection and timely intervention. We addressed the following research question and objectives: Can the microbiota of saliva serve as a non-invasive diagnostic tool for the early detection and monitoring of both oral and non-oral diseases? To achieve this, we will explore the normal flora of microorganisms in the oral cavity, the impact of microbial dysbiosis, and the potential of using specific pathogenic microorganisms as biomarkers. Additionally, we will investigate the correlation between oral and non-oral diseases by analyzing total saliva or site-specific dental biofilms for signs of symbiosis or dysbiosis. This research seeks to contribute valuable insights into the development of a non-invasive diagnostic approach with broad applications in healthcare.

RevDate: 2024-07-15

Zhao B, Li C, Hu T, et al (2024)

Robust {Pb10}-Cluster-Based Metal-Organic Framework for Capturing and Converting CO2 into Cyclic Carbonates under Mild Conditions.

Inorganic chemistry [Epub ahead of print].

Developing a highly active catalyst that can efficiently capture and convert carbon dioxide (CO2) into high-value-added energy materials remains a severe challenge, which inspires us to explore effective metal-organic frameworks (MOFs) with high chemical stability and high-density active sites. Herein, we report a robust 3D lead(II)-organic framework of {(Me2NH2)2[Pb5(PTTPA)2(H2O)3]·2DMF·3H2O}n (NUC-111) with unreported [Pb10(COO)22(H2O)6] clusters (abbreviated as {Pb10}) as nodes (H6PTTPA = 4,4',4″-(pyridine-2,4,6-triyl)triisophthalic acid). After thermal activation, NUC-111a is functionalized by the multifarious symbiotic acid-base active sites of open Pb[2+] sites and uncoordinated pyridine groups on the inner surface of the void volume. Gas adsorption tests confirm that NUC-111a displays a higher separation performance for mixed gases of f CO2 and CH4 with the selectivity of CO2/CH4 at 273 K and 101 kPa being 31 (1:99, v/v), 23 (15:85, v/v), and 8 (50:50, v/v), respectively. When the temperature rises to 298 K, the selectivity of CO2/CH4 at 101 kPa is 26 (1:99, v/v), 22 (15:85, v/v), and 11 (50:50, v/v). Moreover, activated NUC-111a exhibited excellent catalytic performance, stability, and recyclability for the cycloaddition of CO2 with epoxides under mild conditions. Hence, this work provides valuable insight into designing MOFs with multifunctionality for CO2 capture, separation, and conversion.

RevDate: 2024-07-15
CmpDate: 2024-07-15

Shoji F (2024)

[The Role of Gut Microbiota in Lung Carcinogenesis and Cancer Immunotherapy].

Gan to kagaku ryoho. Cancer & chemotherapy, 51(6):597-602.

In recent years, the human microbiota, especially the gut microbiota, has been attracting attention in various fields, and it is one of the topics in the field of oncology. The human microbiota is known to act directly or indirectly on host immunity, and the gut and lung microbiota influence each other through the"gut-lung axis". It has been suggested that dysbiosis, a condition in which the symbiosis of the human microbiota is disrupted, induces lung inflammation and various respiratory diseases, and is also implicated in the immune microenvironment of lung cancer. It is also widely known that the gut microbiota modulates the efficacy of cancer immunotherapy, a major pillar of lung cancer treatment, and many clinical trials targeting the gut microbiota, such as fecal microbiome transplantation and biotics intervention, are currently being conducted. In the future, research on lung carcinogenesis mechanisms and lung cancer treatment focusing on the human microbiota will become increasingly active.

RevDate: 2024-07-15
CmpDate: 2024-07-15

Bonetto M, Cofré N, Calvo F, et al (2024)

Effects of arbuscular mycorrhizal fungi in the rhizosphere of two olive (Olea europaea) varieties Arbequina and Barnea under water deficit conditions.

Functional plant biology : FPB, 51:.

One strategy to improve olive (Olea europaea) tree drought tolerance is through the symbiosis of arbuscular mycorrhizal fungi (AMF), which helps alleviate water deficit through a combination of morphophysiological effects. Cuttings of olive varieties Arbequina (A) and Barnea (B) were grown with (+AMF) or without (-AMF) inoculum in the olive grove rhizosphere soil. One year after establishment, pots were exposed to four different water regimes: (1) control (100% of crop evapotranspiration); (2) short-period drought (20days); (3) long-period drought (25days); and (4) rewatering (R). To evaluate the influence of AMF on tolerance to water stress, stem water potential, stomatal conductance and the biomarkers for water deficit malondialdehyde, proline, soluble sugars, phenols, and flavonoids were evaluated at the end of the irrigation regimes. Stem water potential showed higher values in A(+) and B(+) in all water conditions, and the opposite was true for stomatal conductance. For proline and soluble sugars, the stem water potential trend is repeated with some exceptions. AMF inoculum spore communities from A(+ and -) and B(+ and -) were characterised at the morphospecies level in terms of richness and abundance. Certain morphospecies were identified as potential drought indicators. These results highlight that the benefits of symbiotic relationships between olive and native AMF can help to mitigate the effects of abiotic stress in soils affected by drought.

RevDate: 2024-07-15

Sin WC, Liu J, Zhong JY, et al (2024)

Comparative proteomics analysis of root and nodule mitochondria of soybean.

Plant, cell & environment [Epub ahead of print].

Legumes perform symbiotic nitrogen fixation through rhizobial bacteroids housed in specialised root nodules. The biochemical process is energy-intensive and consumes a huge carbon source to generate sufficient reducing power. To maintain the symbiosis, malate is supplied by legume nodules to bacteroids as their major carbon and energy source in return for ammonium ions and nitrogenous compounds. To sustain the carbon supply to bacteroids, nodule cells undergo drastic reorganisation of carbon metabolism. Here, a comprehensive quantitative comparison of the mitochondrial proteomes between root nodules and uninoculated roots was performed using data-independent acquisition proteomics, revealing the modulations in nodule mitochondrial proteins and pathways in response to carbon reallocation. Corroborated our findings with that from the literature, we believe nodules preferably allocate cytosolic phosphoenolpyruvates towards malate synthesis in lieu of pyruvate synthesis, and nodule mitochondria prefer malate over pyruvate as the primary source of NADH for ATP production. Moreover, the differential regulation of respiratory chain-associated proteins suggests that nodule mitochondria could enhance the efficiencies of complexes I and IV for ATP synthesis. This study highlighted a quantitative proteomic view of the mitochondrial adaptation in soybean nodules.

RevDate: 2024-07-15

Zhang X, Luo Z, Marand AP, et al (2024)

A spatially resolved multiomic single-cell atlas of soybean development.

bioRxiv : the preprint server for biology pii:2024.07.03.601616.

Cis -regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.

RevDate: 2024-07-15

Cabuslay C, Wertz JT, Béchade B, et al (2024)

Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants.

Molecular ecology [Epub ahead of print].

The evolution of animals and their gut symbionts is a complex phenomenon, obscured by lability and diversity. In social organisms, transmission of symbionts among relatives may yield systems with more stable associations. Here, we study the history of a social insect symbiosis involving cephalotine ants and their extracellular gut bacteria, which come predominantly from host-specialized lineages. We perform multi-locus phylogenetics for symbionts from nine bacterial orders, and map prior amplicon sequence data to lineage-assigned symbiont genomes, studying distributions of rigorously defined symbionts across 20 host species. Based on monophyly and additional hypothesis testing, we estimate that these specialized gut bacteria belong to 18 distinct lineages, of which 15 have been successfully isolated and cultured. Several symbiont lineages showed evidence for domestication events that occurred later in cephalotine evolutionary history, and only one lineage was ubiquitously detected in all 20 host species and 48 colonies sampled with amplicon 16S rRNA sequencing. We found evidence for phylogenetically constrained distributions in four symbionts, suggesting historical or genetic impacts on community composition. Two lineages showed evidence for frequent intra-lineage co-infections, highlighting the potential for niche divergence after initial domestication. Nearly all symbionts showed evidence for occasional host switching, but four may, more often, co-diversify with their hosts. Through our further assessment of symbiont localization and genomic functional profiles, we demonstrate distinct niches for symbionts with shared evolutionary histories, prompting further questions on the forces underlying the evolution of hosts and their gut microbiomes.

RevDate: 2024-07-16
CmpDate: 2024-07-13

Kodama Y, Kitatani A, Y Morita (2024)

Characterization of Crystals in Ciliate Paramecium bursaria Harboring Endosymbiotic Chlorella variabilis.

Current microbiology, 81(9):265.

Protists, including ciliates retain crystals in their cytoplasm. However, their functions and properties remain unclear. To comparatively analyze the crystals of Paramecium bursaria, a ciliate, associated with and without the endosymbiotic Chlorella variabilis, we investigated the isolated crystals using a light microscope and analyzed their length and solubility. A negligible number of crystals was found in P. bursaria cells harboring symbiotic algae. The average crystal length in alga-free and algae-reduced cells was about 6.8 μm and 14.4 μm, respectively. The crystals of alga-free cells were spherical, whereas those of algae-reduced cells were angular in shape. The crystals of alga-free cells immediately dissolved in acids and bases, but not in water or organic solvents, and were stable at - 20 °C for more than 3 weeks. This study, for the first time, reveals that the characteristics of crystals present in the cytoplasm of P. bursaria vary greatly depending on the amount of symbiotic algae.

RevDate: 2024-07-13
CmpDate: 2024-07-13

Park Y, Kim W, Cha Y, et al (2024)

Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa.

Harmful algae, 137:102680.

High levels of environmental H2O2 represent a threat to many freshwater bacterial species, including toxic-bloom-forming Microcystis aeruginosa, particularly under high-intensity light conditions. The highest extracellular catalase activity-possessing Pseudoduganella aquatica HC52 was chosen among 36 culturable symbiotic isolates from the phycosphere in freshly collected M. aeruginosa cells. A zymogram for catalase activity revealed the presence of only one extracellular catalase despite the four putative catalase genes (katA1, katA2, katE, and srpA) identified in the newly sequenced genome (∼6.8 Mb) of P. aquatica HC52. Analysis of secreted catalase using liquid chromatography-tandem mass spectrometry was identified as KatA1, which lacks a typical signal peptide, although the underlying mechanism for its secretion is unknown. The expression of secreted KatA1 appeared to be induced in the presence of H2O2. Proteomic analysis also confirmed the presence of KatA1 inside the outer membrane vesicles secreted by P. aquatica HC52 following exposure to H2O2. High light intensities (> 100 µmol m[-2] s[-1]) are known to kill catalase-less axenic M. aeruginosa cells, but the present study found that the presence of P. aquatica cells supported the growth of M. aeruginosa, while the extracellular catalases in supernatant or purified form also sustained the growth of M. aeruginosa under the same conditions. Our results suggest that the extracellular catalase secreted by P. aquatica HC52 enhances the tolerance of M. aeruginosa to H2O2, thus promoting the formation of M. aeruginosa blooms under high light intensities.

RevDate: 2024-07-13
CmpDate: 2024-07-13

Li R, Deng Y, Shang L, et al (2024)

Evidence for the production of asexual resting cysts in a free-living species of Symbiodiniaceae (Dinophyceae).

Harmful algae, 137:102658.

Coral reef ecosystems are the most productive and biodiverse marine ecosystems, with their productivity levels highly dependent on the symbiotic dinoflagellates belonging to the family Symbiodiniaceae. As a unique life history strategy, resting cyst production is of great significance in the ecology of many dinoflagellate species, those HABs-causing species in particular, however, there has been no confirmative evidence for the resting cyst production in any species of the family Symbiodiniaceae. Based on morphological and life history observations of cultures in the laboratory and morpho-molecular detections of cysts from the marine sediments via fluorescence in situ hybridization (FISH), cyst photography, and subsequent singe-cyst PCR sequencing, here we provide evidences for the asexual production of resting cysts by Effrenium voratum, the free-living, red tide-forming, and the type species of the genus Effrenium in Symbiodiniaceae. The evidences from the marine sediments were obtained through a sequential detections: Firstly, E. voratum amplicon sequence variants (ASVs) were detected in the cyst assemblages that were concentrated with the sodium polytungstate (SPT) method from the sediments collected from different regions of China Seas by high-throughput next generation sequencing (NGS); Secondly, the presence of E. voratum in the sediments was detected by PCR using the species-specific primers for the DNA directly extracted from sediment; Thirdly, E. voratum cysts were confirmed by a combined approach of FISH using the species-specific probes, light microscopic (LM) photography of the FISH-positive cysts, and a subsequent single-cyst PCR sequencing for the FISH-positive and photographed cysts. The evidences from the laboratory-reared clonal cultures of E. voratum include that: 1) numerous cysts formed in the two clonal cultures and exhibited a spherical shape, a smooth surface, absence of ornaments, and a large red accumulation body; 2) cysts could maintain morphologically intact for a storage of two weeks to six months at 4 °C in darkness and of which 76-92 % successfully germinated through an internal development processes within a time period of 3-21 days after being transferred back to the normal culturing conditions; 3) two or four germlings were released from each cyst through the cryptopylic archeopyle in all cysts with continuous observations of germination processes; and 4) while neither sexual mating of gametes nor planozygote (cells with two longitudinal flagella) were observed, the haploidy of cysts was proven with flow cytometric measurements and direct LM measurements of fluorescence from cells stained with either propidium iodide (PI) or DAPI, which together suggest that the cysts were formed asexually. All evidences led to a conclusion that E. voratum is capable of producing asexual resting cysts, although its sexuality cannot be completely excluded, which guarantees a more intensive investigation. This work fills a gap in the knowledge about the life cycle, particularly the potential of resting cyst formation, of the species in Symbiodiniaceae, a group of dinoflagellates having unique life forms and vital significance in the ecology of coral reefs, and may provide novel insights into understanding the recovery mechanisms of coral reefs destructed by the global climate change and suggest various forms of resting cysts in the cyst assemblages of dinoflagellates observed in the field sediments, including HABs-causing species.

RevDate: 2024-07-13

Yu Q, Chen J, Ye M, et al (2024)

N-acyl homoserine lactones (AHLs) enhanced removal of cadmium and other pollutants by algae-bacteria consortia.

Journal of environmental management, 366:121792 pii:S0301-4797(24)01778-X [Epub ahead of print].

Signal transduction is an important mode of algae-bacteria interaction, in which bacterial quorum sensing (QS) may affect microalgal growth and metabolism. Currently, little is known whether acyl homoserine lactones (AHLs) released by bacteria can affect the pollutant removal by algae-bacteria consortia (ABC). In this study, we constructed ABC using Chlorella vulgaris (Cv) with two AHLs-producing bacteria and investigated their performance in the removal of multiple pollutants, including chemical oxygen demand (COD), total nitrogen (TN), phosphorus (P), and cadmium (Cd). The AHLs-producing bacteria, namely Agrobacterium sp. (Ap) and Ensifer adherens (Ea), were capable of forming a symbiosis with C. vulgaris. Consortia of Cv and Ap with ratio of 2:1 (Cv2-Ap1) showed the optimal growth promotion and higher removal of Cd, COD, TN, and P compared to the C. vulgaris monoculture. Cv2-Ap1 ABC removed 36.1-47.5% of Cd, 94.5%-94.6% COD, 37.1%-56.0% TN, and 90.4%-93.5% P from the culture medium. In addition, increase of intracellular neutral lipids and extracellular protein, as well as the types of functional groups on cell surface contributed to Cd removal and tolerance in the Cv2-Ap1 ABC. Six AHLs were detected in the Cv2-Ap1 culture. Among these, 3OC8-HSL and 3OC12-HSL additions promoted the ABC growth and enhanced their Cd accumulation. These findings may contribute to further understanding of AHL-mediated communication between algae and bacteria and provide support bioremediation efforts of metal-containing wastewater.

RevDate: 2024-07-16

Smith J, Yeluripati J, Smith P, et al (2020)

Potential yield challenges to scale-up of zero budget natural farming.

Nature sustainability, 3:247-252.

Under current trends, 60% of India's population (>10% of people on Earth) will experience severe food deficiencies by 2050. Increased production is urgently needed, but high costs and volatile prices are driving farmers into debt. Zero budget natural farming (ZBNF) is a grassroots movement that aims to improve farm viability by reducing costs. In Andhra Pradesh alone, 523,000 farmers have converted 13% of productive agricultural area to ZBNF. However, sustainability of ZBNF is questioned because external nutrient inputs are limited, which could cause a crash in food production. Here, we show that ZBNF is likely to reduce soil degradation and could provide yield benefits for low-input farmers. Nitrogen fixation, either by free-living nitrogen fixers in soil or symbiotic nitrogen fixers in legumes, is likely to provide the major portion of nitrogen available to crops. However, even with maximum potential nitrogen fixation and release, only 52-80% of the national average nitrogen applied as fertilizer is expected to be supplied. Therefore, in higher-input systems, yield penalties are likely. Since biological fixation from the atmosphere is possible only with nitrogen, ZBNF could limit the supply of other nutrients. Further research is needed in higher-input systems to ensure that mass conversion to ZBNF does not limit India's capacity to feed itself.

RevDate: 2024-07-13

Williams TA, Davin AA, Szánthó LL, et al (2024)

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.

The ISME journal pii:7713227 [Epub ahead of print].

In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.

RevDate: 2024-07-15
CmpDate: 2024-07-13

Kozlova AP, Muntyan VS, Vladimirova ME, et al (2024)

Soil Giant Phage: Genome and Biological Characteristics of Sinorhizobium Jumbo Phage.

International journal of molecular sciences, 25(13):.

This paper presents the first in-depth research on the biological and genomic properties of lytic rhizobiophage AP-J-162 isolated from the soils of the mountainous region of Dagestan (North Caucasus), which belongs to the centers of origin of cultivated plants, according to Vavilov N.I. The rhizobiophage host strains are nitrogen-fixing bacteria of the genus Sinorhizobium spp., symbionts of leguminous forage grasses. The phage particles have a myovirus virion structure. The genome of rhizobiophage AP-J-162 is double-stranded DNA of 471.5 kb in length; 711 ORFs are annotated and 41 types of tRNAs are detected. The closest phylogenetic relative of phage AP-J-162 is Agrobacterium phage Atu-ph07, but no rhizobiophages are known. The replicative machinery, capsid, and baseplate proteins of phage AP-J-162 are structurally similar to those of Escherichia phage T4, but there is no similarity between their tail protein subunits. Amino acid sequence analysis shows that 339 of the ORFs encode hypothetical or functionally relevant products, while the remaining 304 ORFs are unique. Additionally, 153 ORFs are similar to those of Atu_ph07, with one-third of the ORFs encoding different enzymes. The biological properties and genomic characteristics of phage AP-J-162 distinguish it as a unique model for exploring phage-microbe interactions with nitrogen-fixing symbiotic microorganisms.

RevDate: 2024-07-15
CmpDate: 2024-07-13

Daminova AG, Leksin IY, Khabibrakhmanova VR, et al (2024)

The Roles of the Anthraquinone Parietin in the Tolerance to Desiccation of the Lichen Xanthoria parietina: Physiology and Anatomy of the Pale and Bright-Orange Thalli.

International journal of molecular sciences, 25(13):.

Lichens are symbiotic organisms that effectively survive in harsh environments, including arid regions. Maintaining viability with an almost complete loss of water and the rapid restoration of metabolism during rehydration distinguishes lichens from most eukaryotic organisms. The lichen Xanthoria parietina is known to have high stress tolerance, possessing diverse defense mechanisms, including the presence of the bright-orange pigment parietin. While several studies have demonstrated the photoprotective and antioxidant properties of this anthraquinone, the role of parietin in the tolerance of lichens to desiccation is not clear yet. Thalli, which are exposed to solar radiation and become bright orange, may require enhanced desiccation tolerance. Here, we showed differences in the anatomy of naturally pale and bright-orange thalli of X. parietina and visualized parietin crystals on the surface of the upper cortex. Parietin was extracted from bright-orange thalli by acetone rinsing and quantified using HPLC. Although acetone rinsing did not affect PSII activity, thalli without parietin had higher levels of lipid peroxidation and a lower membrane stability index in response to desiccation. Furthermore, highly pigmented thalli possess thicker cell walls and, according to thermogravimetric analysis, higher water-holding capacities than pale thalli. Thus, parietin may play a role in desiccation tolerance by stabilizing mycobiont membranes, providing an antioxidative defense, and changing the morphology of the upper cortex of X. parietina.

RevDate: 2024-07-15
CmpDate: 2024-07-13

Dong M, He J, Tang X, et al (2024)

Genome-Wide Identification of the Sulfate Transporters Gene Family in Blueberry (Vaccinium spp.) and Its Response to Ericoid Mycorrhizal Fungi.

International journal of molecular sciences, 25(13):.

Sulfur metabolism plays a major role in plant growth and development, environmental adaptation, and material synthesis, and the sulfate transporters are the beginning of sulfur metabolism. We identified 37 potential VcSULTR genes in the blueberry genome, encoding peptides with 534 to 766 amino acids. The genes were grouped into four subfamilies in an evolutionary analysis. The 37 putative VcSULTR proteins ranged in size from 60.03 to 83.87 kDa. These proteins were predicted to be hydrophobic and mostly localize to the plasma membrane. The VcSULTR genes were distributed on 30 chromosomes; VcSULTR3;5b and VcSULTR3;5c were the only tandemly repeated genes. The VcSULTR promoters contained cis-acting elements related to the fungal symbiosis and stress responses. The transcript levels of the VcSULTRs differed among blueberry organs and changed in response to ericoid mycorrhizal fungi and sulfate treatments. A subcellular localization analysis showed that VcSULTR2;1c localized to, and functioned in, the plasma membrane and chloroplast. The virus-induced gene knock-down of VcSULTR2;1c resulted in a significantly decreased endogenous sulfate content, and an up-regulation of genes encoding key enzymes in sulfur metabolism (VcATPS2 and VcSiR1). These findings enhance our understanding of mycorrhizal-fungi-mediated sulfate transport in blueberry, and lay the foundation for further research on blueberry-mycorrhizal symbiosis.

RevDate: 2024-07-15

Markova O, Garipova S, Chistoedova A, et al (2024)

Predicting Field Effectiveness of Endophytic Bacillus subtilis Inoculants for Common Bean Using Morphometric and Biochemical Markers.

Plants (Basel, Switzerland), 13(13):.

According to four field experiments, after the inoculation of Phaseolus vulgaris L. cultivar Ufimskaya with the commercial strain Bacillus subtilis 26D and the promising strain B. subtilis 10-4, it was found that inoculation with B. subtilis 10-4 improved seed productivity (SP) by 31-41% per plant, but only in dry years. In contrast, all 4 years of inoculation with B. subtilis 26D were ineffective or neutral. It was intended to determine the growing and biochemical characteristics of inoculated 7-day-old plants, which correlate with the field SP of bacterial preparations. The SP of inoculated plants (average of 4 years) correlated with root length (0.83), MDA content (-0.98), and catalase (CAT) activity in roots (-0.96) of week-old seedlings. High correlation coefficients between the H2O2 content in the roots and SP (0.89 and 0.77), as well as between the H2O2 content in shoots and SP (0.98 and 0.56), were observed only in two dry years, when the influence of bacteria was detected. These physiological indicators were identified as potential markers for predicting the effectiveness of the endophytic symbiosis between bean plants and B. subtilis strains. The findings may be used to develop effective microbial-based, eco-friendly technologies for bean production.

RevDate: 2024-07-15

Morales D, de la Fuente-Nieto L, Marco P, et al (2024)

Elaboration and Characterization of Novel Kombucha Drinks Based on Truffles (Tuber melanosporum and Tuber aestivum) with Interesting Aromatic and Compositional Profiles.

Foods (Basel, Switzerland), 13(13):.

The organoleptic and bioactive properties of truffles place these fungi as interesting materials for use in the of design functional foods based on fruiting bodies outside commercial standards. Moreover, kombucha beverages have become more popular in the Western world, leading to novel drinks using alternative substrates instead of tea leaves. In this work, two truffle species (Tuber melanosporum, TMEL; Tuber aestivum, TAES) and three different symbiotic consortia of bacteria and yeasts (SCOBYs: SC1, SC2, and SC3) were tested. Fermentation (21 days) was monitored in terms of physicochemical (pH, viscosity), biochemical (total carbohydrates, alcohol, soluble proteins, phenolic compounds), and sensory attributes (volatile organic compounds, VOCs). The obtained pH ranges were adequate, alcohol levels were undetectable or very low, and sugar content was lower than in traditional kombuchas or other beverages. In most cases, the usual bottling time could be applied (7-10 days), although longer fermentations are recommended (14 days) to reach higher protein and phenolic compounds contents. Truffle kombuchas produced up to 51 volatile organic compounds (alcohols, acids, esters, ketones, and aldehydes, among others), with TMEL showing a more complex profile than TAES. During the first week, acidic compound production was observed, especially acetic acid. Similar behavior in the VOC profile was reported with different SCOBYs.

RevDate: 2024-07-15

Wu D, Hao L, Liu X, et al (2024)

The Anti-Biofilm Properties of Phloretin and Its Analogs against Porphyromonas gingivalis and Its Complex Flora.

Foods (Basel, Switzerland), 13(13):.

Porphyromonas gingivalis is crucial for the pathogenesis of periodontitis. This research investigated the effects of the fruit-derived flavonoid phloretin and its analogs on the growth of pure P. gingivalis and the flora of P. gingivalis mixed with the symbiotic oral pathogens Fusobacterium nucleatum and Streptococcus mitis. The results showed that the tested flavonoids had little effect on the biofilm amount of pure P. gingivalis, but significantly reduced the biofilm amount of mixed flora to 83.6~89.1%. Biofilm viability decreased to 86.7~92.8% in both the pure- and mixed-bacterial groups after naringenin and phloretin treatments. SEM showed that phloretin and phlorizin displayed a similar and remarkable destructive effect on P. gingivalis and the mixed biofilms. Transcriptome analysis confirmed that biofilm formation was inhibited by these flavonoids, and phloretin significantly regulated the transcription of quorum sensing. Phlorizin and phloretin reduced AI-2 activity to 45.9% and 55.4%, respectively, independent of the regulation of related gene transcription. This research marks the first finding that these flavonoids possess anti-biofilm properties against P. gingivalis and its intricate bacterial community, and the observed performance variations, driven by structural differences, underscore the existence of intriguing structure-activity relationships.

RevDate: 2024-07-12

Xu C, Zhao X, Duan H, et al (2024)

Synergistic enzymatic mechanism of lepidolite leaching enhanced by a mixture of Bacillus mucilaginosus and Bacillus circulans.

The Science of the total environment pii:S0048-9697(24)04860-5 [Epub ahead of print].

Numerous studies have demonstrated that the co-leaching of ores by different silicate bacteria significantly improves the performance of bioleaching systems. Nevertheless, the mechanism of different silicate bacteria synergistically or complementarily enhanced the leaching process of lithium-containing silicate remains unclear. This study discussed the leaching impact of the combined presence of two metabolically distinct silicate bacteria on lepidolite, with the aim of comprehending the synergistic effect resulting from the presence of Bacillus mucilaginosus and Bacillus circulans in the leaching process. The results indicated that the polysaccharides and proteins secreted by bacteria-containing functional groups such as -OH and -COOH, which played an important role in the complex decomposition of ores. Organic acids played the role of acid etching and complexation. Bacillus mucilaginosus and Bacillus circulans exhibited low individual leaching efficiency, primarily due to their weak organic acid secretion. Moreover, the prolific polysaccharide production by Bacillus mucilaginosus led to bacterial aggregation, diminishing contact capability with minerals. Bacillus circulans decomposed the excessive polysaccharides produced by Bacillus mucilaginosus through enzymatic hydrolysis in the co-bioleaching process, providing later nutrient supply for both strains. The symbiosis of the two strains enhanced the synthesis and metabolic capabilities of both strains, resulting in increased organic acid secretion. In addition, protein and humic acid production by Bacillus mucilaginosus intensified, collectively enhancing the leaching efficiency. These findings suggested that the primary metabolic products secreted by different bacterial strains in the leaching process differ. The improvement in bioleaching efficiency during co-leaching was attributed to their effective synergistic metabolism. This work contributes to the construction of an efficient engineering microbial community to improve the efficiency of silicate mineral leaching, and reveals the feasibility of microbial co-culture to improve bioleaching.

RevDate: 2024-07-12

Qian F, Liu Y, He L, et al (2024)

Metagenomic insights into microbial metabolic mechanisms of a combined solid-phase denitrification and anammox process for nitrogen removal in mainstream wastewater treatment.

Journal of environmental management, 366:121797 pii:S0301-4797(24)01783-3 [Epub ahead of print].

To overcome the significant challenges associated with nitrite supply and nitrate residues in mainstream anaerobic ammonium oxidation (anammox)-based processes, this study developed a combined solid-phase denitrification (SPD) and anammox process for low-strength nitrogen removal without the addition of nitrite. The SPD step was performed in a packed-bed reactor containing poly-3-hydroxybutyrate-co-3-hyroxyvelate (PHBV) prior to employing the anammox granular sludge reactor in the continuous-flow mode. The removal efficiency of total inorganic nitrogen reached 95.7 ± 1.2% under a nitrogen loading rate of 0.18 ± 0.01 kg N·m[3]·d[-1], and it required 1.02 mol of nitrate to remove 1 mol of ammonium nitrogen. The PHBV particles not only served as biofilm carriers for the symbiosis of hydrolytic bacteria (HB) and denitrifying bacteria (DB), but also carbon sources that facilitated the coupling of partial denitrification and anammox in the granules. Metagenomic sequencing analysis indicated that Burkholderiales was the most abundant HB genus in SPD. The metabolic correlations between DB (Betaproteobacteria, Rhodocyclaceae, and Anaerolineae) and anammox bacteria (Candidatus Brocadiac and Kuenenia) in the granules were confirmed through microbial co-occurrence networks analysis and functional gene annotations. Additionally, the genes encoding nitrate reductase (Nap) and nitrite reductase (Nir) in DB primarily facilitated nitrate reduction, thereby supplying nitric oxide to anammox bacteria for subsequent nitrogen removal with hydrazine synthase (Hzs) and hydrazine dehydrogenase (Hdh). The findings provide insights into microbial metabolism within combined SPD and anammox processes, thus advancing the development of mainstream anammox-based processes in engineering applications.

RevDate: 2024-07-12

da Silva AF, Machado LC, da Silva LMI, et al (2024)

Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil.

Journal of virology [Epub ahead of print].

UNLABELLED: Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments.

IMPORTANCE: Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.

RevDate: 2024-07-12

Jandl B, Dighe S, Gasche C, et al (2024)

Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities.

Clinical microbiology reviews [Epub ahead of print].

SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.

RevDate: 2024-07-12
CmpDate: 2024-07-12

Almalla A, Alzain N, Elomaa L, et al (2024)

Hydrogel-Integrated Millifluidic Systems: Advancing the Fabrication of Mucus-Producing Human Intestinal Models.

Cells, 13(13):.

The luminal surface of the intestinal epithelium is protected by a vital mucus layer, which is essential for lubrication, hydration, and fostering symbiotic bacterial relationships. Replicating and studying this complex mucus structure in vitro presents considerable challenges. To address this, we developed a hydrogel-integrated millifluidic tissue chamber capable of applying precise apical shear stress to intestinal models cultured on flat or 3D structured hydrogel scaffolds with adjustable stiffness. The chamber is designed to accommodate nine hydrogel scaffolds, 3D-printed as flat disks with a storage modulus matching the physiological range of intestinal tissue stiffness (~3.7 kPa) from bioactive decellularized and methacrylated small intestinal submucosa (dSIS-MA). Computational fluid dynamics simulations were conducted to confirm a laminar flow profile for both flat and 3D villi-comprising scaffolds in the physiologically relevant regime. The system was initially validated with HT29-MTX seeded hydrogel scaffolds, demonstrating accelerated differentiation, increased mucus production, and enhanced 3D organization under shear stress. These characteristic intestinal tissue features are essential for advanced in vitro models as they critically contribute to a functional barrier. Subsequently, the chamber was challenged with human intestinal stem cells (ISCs) from the terminal ileum. Our findings indicate that biomimicking hydrogel scaffolds, in combination with physiological shear stress, promote multi-lineage differentiation, as evidenced by a gene and protein expression analysis of basic markers and the 3D structural organization of ISCs in the absence of chemical differentiation triggers. The quantitative analysis of the alkaline phosphatase (ALP) activity and secreted mucus demonstrates the functional differentiation of the cells into enterocyte and goblet cell lineages. The millifluidic system, which has been developed and optimized for performance and cost efficiency, enables the creation and modulation of advanced intestinal models under biomimicking conditions, including tunable matrix stiffness and varying fluid shear stresses. Moreover, the readily accessible and scalable mucus-producing cellular tissue models permit comprehensive mucus analysis and the investigation of pathogen interactions and penetration, thereby offering the potential to advance our understanding of intestinal mucus in health and disease.

RevDate: 2024-07-12

Heidari H, DA Lawrence (2024)

An integrative exploration of environmental stressors on the microbiome-gut-brain axis and immune mechanisms promoting neurological disorders.

Journal of toxicology and environmental health. Part B, Critical reviews [Epub ahead of print].

The microbiome-gut-brain axis is altered by environmental stressors such as heat, diet, and pollutants as well as microbes in the air, water, and soil. These stressors might alter the host's microbiome and symbiotic relationship by modifying the microbial composition or location. Compartmentalized mutualistic microbes promote the beneficial interactions in the host leading to circulating metabolites and hormones such as insulin and leptin that affect inter-organ functions. Inflammation and oxidative stress induced by environmental stressors may alter the composition, distribution, and activities of the microbes in the microbiomes such that the resultant metabolite and hormone changes are no longer beneficial. The microbiome-gut-brain axis and immune adverse changes that may accompany environmental stressors are reviewed for effects on innate and adaptive immune cells, which may make host immunity less responsive to pathogens and more reactive to self-antigens. Cardiovascular and fluid exchanges to organs might adversely alter organ functionality. Organs, especially the brain, need a consistent supply of nutrients and clearance of debris; disruption of these exchanges by stressors, and involvement of gut microbiome are discussed regarding neural dysfunctions with Alzheimer's disease, autistic spectrum disorders, viral infections, and autoimmune diseases. The focus of this review includes the manner in which environmental stressors may disrupt gut microbiota leading to adverse immune and hormonal influences on development of neuropathology related to hyperhomocysteinemia, inflammation, and oxidative stress, and how certain therapeutics may be beneficial. Strategies are explored to lessen detrimental effects of environmental stressors on central and peripheral health navigated toward (1) understanding neurological disorders and (2) promoting environmental and public health and well-being.

RevDate: 2024-07-12

Zeghina I, El Ouar I, Tartouga MA, et al (2024)

GC-MS Profiling and Pharmacological Potential of Physconia venusta (Ach.) Poelt.

Turkish journal of pharmaceutical sciences, 21(3):243-251.

OBJECTIVES: Lichens are complex symbiotic organisms that generate various bioactive compounds with significant therapeutic value. We investigated the chemical composition and bioactivity of the acetone extract of the Algerian lichen Physconia venusta (Ach.) poet.

MATERIALS AND METHODS: Phytochemical screening was performed using gas chromatography-mass spectrometry (GC-MS). The antibacterial activity was assessed against Escherichia coli, Pseudomonas aeruginosa, Salmonella enteritidis, Salmonella typhi, Staphylococcus aureus, Listeria monocytogenes, and Bacillus subtilis using an agar diffusion test with the determination of the minimal inhibition concentration (MIC), while the antioxidant activity was determined using different chemical methods (DPPH, ABTS, CUPRAC, reducing power, superoxide anion scavenging, β-carotene bleaching, and metal chelate). In addition, cytotoxic activity was tested using Artemia salina (Brine shrimp) bioassay.

RESULTS: The studied extract exhibited intense antibacterial activity against E. coli and S. aureus with inhibition diameters of 28 ± 0.01 and 22 ± 0.01 mm, respectively, with a MIC value of 6.25 mg/mL and a selectivity index of 2.8. The obtained extract showed different antioxidant trends depending on the selected assay. GC-MS analysis revealed many secondary metabolites.

CONCLUSION: P. venusta, a type of lichen, is a potential source of bioactive substances that could be used in pharmaceuticals.

RevDate: 2024-07-11

Klimov PB, Hubert J, Erban T, et al (2024)

Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q).

International journal for parasitology pii:S0020-7519(24)00138-3 [Epub ahead of print].

Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.

RevDate: 2024-07-11

Shang X, Liu X, Ma X, et al (2024)

Roles of soil minerals in the degradation of chlorpyrifos and its intermediate by microwave activated peroxymonosulfate.

The Science of the total environment pii:S0048-9697(24)04803-4 [Epub ahead of print].

Soil mineral is one of the important factors that affecting oxidant decomposition and pollutants degradation in soil remediation. In this study, the effects of iron minerals, manganese minerals and clay minerals on the degradation of chlorpyrifos (CPF) and its intermediate product 3,5,6-trichloro-2-pyridinol (TCP) by microwave (MW) activated peroxymonosulfate (PMS) were investigated. As a result, the addition of minerals had slight inhibitory effect on the degradation efficiency of CPF by MW/PMS, but the degradation efficiency of TCP was improved by the addition of some specific minerals, including ferrihydrite, birnessite, and random symbiotic mineral of pyrolusite and ramsdellite (Pyr-Ram). The stronger MW absorption ability of minerals is beneficial for PMS decomposition, but the MW absorption ability of minerals cannot be fully utilized because of the weaker MW radiation intensity under constant temperature conditions. Through electron spin resonance test, quenching experiment and electrochemical experiment, electron transfer, SO4[-] and OH, SO4[-] dominated TCP degradation by MW/PMS with the addition of birnessite, Pyr-Ram and ferrihydrite, respectively. Besides, the adsorption effect of ferrihydrite also enhanced the removal of TCP. The redox of Mn (III)/Mn (IV) or Fe (II)/Fe (III) in manganese/iron minerals participated in the generation of reactive species. In addition, the addition of minerals not only increased the variety of alkyl hydroxylation products of CPF, causing different degradation pathways from CPF to TCP, but also further degraded TCP to dechlorination or hydroxylation products. This study demonstrated the synergistic effect of minerals and MW for PMS activation, provided new insights for the effects of soil properties on soil remediation by MW activated PMS technology.

RevDate: 2024-07-12

Zhang L, Ali A, Su J, et al (2024)

Ammonium nitrogen and phosphorus removal by bacterial-algal symbiotic dynamic sponge bioremediation system in micropolluted water: Operational mechanism and transformation pathways.

The Science of the total environment, 947:174636 pii:S0048-9697(24)04785-5 [Epub ahead of print].

Construct a bacteria-algae symbiotic dynamic sponge bioremediation system to simultaneously remove multiple pollutants under micro-pollution conditions. The average removal efficiencies of NH4[+]-N, PO4[3-]-P, total nitrogen (TN), and Ca[2+] were 98.35, 78.74, 95.64, and 84.92 %, respectively. Comparative studies with Auxenochlorella sp. sponge and bacterial sponge bioremediation system confirmed that NH4[+]-N and TN were mainly removed by bacterial heterotrophic nitrification - aerobic denitrification (HN-AD). PO4[3-]-P was removed by algal assimilation and the generation of Ca3(PO4)2 and Ca5(PO4)3OH, and Ca[2+] was removed by algal electron transfer formation of precipitates and microbially induced calcium precipitation (MICP) by bacteria. Algae provided an aerobic environment for the bacterial HN-AD process through photosynthesis, while respiration produced CO2 and adsorbed Ca[2+] to promote the formation of calcium precipitates. Immobilization of Ca[2+] with microalgae via bacterial MICP helped to lift microalgal photoinhibition. The bioremediation system provides theoretical support for research on micropolluted water treatment while increasing phosphorus recovery pathways.

RevDate: 2024-07-11
CmpDate: 2024-07-11

Ma C, Wang J, Gao Y, et al (2024)

The type III effector NopL interacts with GmREM1a and GmNFR5 to promote symbiosis in soybean.

Nature communications, 15(1):5852.

The establishment of symbiotic interactions between leguminous plants and rhizobia requires complex cellular programming activated by Rhizobium Nod factors (NFs) as well as type III effector (T3E)-mediated symbiotic signaling. However, the mechanisms by which different signals jointly affect symbiosis are still unclear. Here we describe the mechanisms mediating the cross-talk between the broad host range rhizobia Sinorhizobium fredii HH103 T3E Nodulation Outer Protein L (NopL) effector and NF signaling in soybean. NopL physically interacts with the Glycine max Remorin 1a (GmREM1a) and the NFs receptor NFR5 (GmNFR5) and promotes GmNFR5 recruitment by GmREM1a. Furthermore, NopL and NF influence the expression of GmRINRK1, a receptor-like kinase (LRR-RLK) ortholog of the Lotus RINRK1, that mediates NF signaling. Taken together, our work indicates that S. fredii NopL can interact with the NF signaling cascade components to promote the symbiotic interaction in soybean.

RevDate: 2024-07-11

Serrano K, Tedeschi F, Andersen SU, et al (2024)

Unraveling plant-microbe symbioses using single-cell and spatial transcriptomics.

Trends in plant science pii:S1360-1385(24)00152-3 [Epub ahead of print].

Plant-microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant-microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells.

RevDate: 2024-07-11

van Leeuwen FWB, Buckle T, van Oosterom MN, et al (2024)

The Rise of Molecular Image-Guided Robotic Surgery.

Journal of nuclear medicine : official publication, Society of Nuclear Medicine pii:jnumed.124.267783 [Epub ahead of print].

Following early acceptance by urologists, the use of surgical robotic platforms is rapidly spreading to other surgical fields. This empowerment of surgical perception via robotic advances occurs in parallel to developments in intraoperative molecular imaging. Convergence of these efforts creates a logical incentive to advance the decades-old image-guided robotics paradigm. This yields new radioguided surgery strategies set to optimally exploit the symbiosis between the growing clinical translation of robotics and molecular imaging. These strategies intend to advance surgical precision by increasing dexterity and optimizing surgical decision-making. In this state-of-the-art review, topic-related developments in chemistry (tracer development) and engineering (medical device development) are discussed, and future scientific robotic growth markets for molecular imaging are presented.

RevDate: 2024-07-11

Dar MA, Xie R, Zabed HM, et al (2024)

Current paradigms and future challenges in harnessing gut bacterial symbionts of insects for biodegradation of plastic wastes.

Insect science [Epub ahead of print].

The ubiquitous incorporation of plastics into daily life, coupled with inefficient recycling practices, has resulted in the accumulation of millions of metric tons of plastic waste, that poses a serious threat to the Earth's sustainability. Plastic pollution, a global problem, disrupts the ecological balance and endangers various life forms. Efforts to combat plastic pollution are underway, with a promising avenue being biological degradation facilitated by certain insects and their symbiotic gut microorganisms, particularly bacteria. This review consolidates existing knowledge on plastic degradation by insects and their influence on gut microbiota. Additionally, it delves into the potential mechanisms employed by insects in symbiosis with gut bacteria, exploring the bioconversion of waste plastics into value-added biodegradable polymers through mineralization. These insights hold significant promise for the bio-upcycling of plastic waste, opening new horizons for future biomanufacturing of high-value chemicals from plastic-derived compounds. Finally, we weigh the pros and cons of future research endeavors related to the bioprospection of plastic-degrading bacteria from underexplored insect species. We also underscore the importance of bioengineering depolymerases with novel characteristics, aiming for their application in the remediation and valorization of waste plastics.

RevDate: 2024-07-11

Stahlhut KN, Neupert DG, Laing JE, et al (2024)

Measuring leaf and root functional traits uncovers multidimensionality of plant responses to arbuscular mycorrhizal fungi.

American journal of botany [Epub ahead of print].

PREMISE: While many studies have measured the aboveground responses of plants to mycorrhizal fungi at a single time point, little is known about how plants respond belowground or across time to mycorrhizal symbiosis. By measuring belowground responses and growth over time in many plant species, we create a more complete picture of how mycorrhizal fungi benefit their hosts.

METHODS: We grew 26 prairie plant species with and without mycorrhizal fungi and measured 14 functional traits to assess above- and belowground tissue quality and quantity responses and changes in resource allocation. We used function-valued trait (FVT) modeling to characterize changes in species growth rate when colonized.

RESULTS: While aboveground biomass responses were positive, the response of traits belowground were much more variable. Changes in aboveground biomass accounted for 60.8% of the variation in mycorrhizal responses, supporting the use of aboveground biomass response as the primary response trait. Responses belowground were not associated with aboveground responses and accounted for 18.3% of the variation. Growth responses over time were highly variable across species. Interestingly, none of the measured responses were phylogenetically conserved.

CONCLUSIONS: Mycorrhizal fungi increase plant growth in most scenarios, but the effects of these fungi belowground and across time are more complicated. This study highlights how differences in plant allocation priorities might affect how they utilize the benefits from mycorrhizal fungi. Identifying and characterizing these differences is a key step to understanding the effects of mycorrhizal mutualisms on whole plant physiology.

RevDate: 2024-07-11

Mashini AG, Oakley CA, Peng L, et al (2024)

Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian-dinoflagellate symbiosis.

The ISME journal pii:7710817 [Epub ahead of print].

Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterised proteomic changes in the native symbiont Breviolum minutum during colonisation of its host sea anemone Exaiptasia diaphana ("Aiptasia"). We also compared the proteome of this native symbiont in the established symbiotic state with that of a non-native symbiont, Durusdinium trenchii. The onset of symbiosis between Aiptasia and Branchioglossum minutum increased accumulation of symbiont proteins associated with acquisition of inorganic carbon and photosynthesis, nitrogen metabolism, micro- and macronutrient starvation, suppression of host immune responses, tolerance to low pH, and management of oxidative stress. Such responses are consistent with a functional, persistent symbiosis. In contrast, D. trenchii predominantly showed elevated levels of immunosuppressive proteins, consistent with the view that this symbiont is an opportunist that forms a less beneficial, less well-integrated symbiosis with this model anemone. By adding symbiont analysis to the already known responses of the host proteome, our results provide a more holistic view of cellular processes that determine host-symbiont specificity and how differences in symbiont partners (i.e., native versus non-native symbionts) may impact the fitness of the cnidarian-dinoflagellate symbiosis.

RevDate: 2024-07-12
CmpDate: 2024-07-10

Ng MS, Soon N, Afiq-Rosli L, et al (2024)

Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity.

Microbial ecology, 87(1):92.

Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.

RevDate: 2024-07-10

Fernández-Pereira C, Leiva C, Luna-Galiano Y, et al (2024)

Improved recycling of a gasification fly ash: An integrated waste management approach within the framework of a Circular Economy.

Waste management (New York, N.Y.), 187:31-38 pii:S0956-053X(24)00384-2 [Epub ahead of print].

A Circular Waste Management alternative is considered in this paper in which a complete ash valorization process is proposed for an Integrated Gasification with Combined Cycle fly ash, trying to extract maximum value from this waste before it is discarded. In the paper, germanium, a scarce resource vital in our modern society, is first extracted from fly ash using water, with an extraction yield of 85%, and subsequently, the leached fly ash is used in the manufacture of fire-resistant boards containing 60% ash, thereby avoiding its disposal in a landfill. The potential environmental impact caused by the two stages of the process was analyzed, and the final effluent was considered to achieve a zero-discharge objective. This paper contributes to the development of a more sustainable management alternative for an industrial waste produced in increased amounts and provides the basis for a symbiotic coupling relationship among various industrial sectors.

RevDate: 2024-07-10
CmpDate: 2024-07-10

Hoffmann G, Lukarska M, Clare RH, et al (2024)

Targeting a microbiota Wolbachian aminoacyl-tRNA synthetase to block its pathogenic host.

Science advances, 10(28):eado1453.

The interplay between humans and their microbiome is crucial for various physiological processes, including nutrient absorption, immune defense, and maintaining homeostasis. Microbiome alterations can directly contribute to diseases or heighten their likelihood. This relationship extends beyond humans; microbiota play vital roles in other organisms, including eukaryotic pathogens causing severe diseases. Notably, Wolbachia, a bacterial microbiota, is essential for parasitic worms responsible for lymphatic filariasis and onchocerciasis, devastating human illnesses. Given the lack of rapid cures for these infections and the limitations of current treatments, new drugs are imperative. Here, we disrupt Wolbachia's symbiosis with pathogens using boron-based compounds targeting an unprecedented Wolbachia enzyme, leucyl-tRNA synthetase (LeuRS), effectively inhibiting its growth. Through a compound demonstrating anti-Wolbachia efficacy in infected cells, we use biophysical experiments and x-ray crystallography to elucidate the mechanism behind Wolbachia LeuRS inhibition. We reveal that these compounds form adenosine-based adducts inhibiting protein synthesis. Overall, our study underscores the potential of disrupting key microbiota to control infections.

RevDate: 2024-07-11

Yuan S, Leng P, Feng Y, et al (2024)

Comparative genomic and transcriptomic analyses provide new insight into symbiotic host specificity.

iScience, 27(7):110207.

Host specificity plays important roles in expanding the host range of rhizobia, while the genetic information responsible for host specificity remains largely unexplored. In this report, the roots of four symbiotic systems with notable different symbiotic phenotypes and the control were studied at four different post-inoculation time points by RNA sequencning (RNA-seq). The differentially expressed genes (DEGs) were divided into "found only in soybean or Lotus," "only expressed in soybean or Lotus," and "expressed in both hosts" according to the comparative genomic analysis. The distributions of enriched function ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways vary significantly in different symbiotic systems. Host specific genes account for the majority of the DEGs involved in response to stimulus, associated with plant-pathogen interaction pathways, and encoding resistance (R) proteins, the symbiotic nitrogen fixation (SNF) proteins and the target proteins in the SNF-related modules. Our findings provided molecular candidates for better understanding the mechanisms of symbiotic host-specificity.

RevDate: 2024-07-11

Jibran R, Tahir J, Andre CM, et al (2024)

DWARF27 and CAROTENOID CLEAVAGE DIOXYGENASE 7 genes regulate release, germination and growth of gemma in Marchantia polymorpha.

Frontiers in plant science, 15:1358745.

Strigolactones (SLs), a class of carotenoid-derived hormones, play a crucial role in flowering plants by regulating underground communication with symbiotic arbuscular mycorrhizal fungi (AM) and controlling shoot and root architecture. While the functions of core SL genes have been characterized in many plants, their roles in non-tracheophyte plants like liverworts require further investigation. In this study, we employed the model liverwort species Marchantia polymorpha, which lacks detectable SL production and orthologs of key SL biosynthetic genes, including CAROTENOID CLEAVAGE DIOXYGENASE 8 (CCD8) and MORE AXILLARY GROWTH 1 (MAX1). However, it retains some SL pathway components, including DWARF27 (D27) and CCD7. To help elucidate the function of these remaining components in M. polymorpha, knockout mutants were generated for MpD27-1, MpD27-2 and MpCCD7. Phenotypic comparisons of these mutants with the wild-type control revealed a novel role for these genes in regulating the release of gemmae from the gemma cup and the germination and growth of gemmae in the dark. Mpd27-1, Mpd27-2, and Mpccd7 mutants showed lower transcript abundance of genes involved in photosynthesis, such as EARLY LIGHT INDUCED (ELI), and stress responses such as LATE EMBRYOGENESIS ABUNDANT (LEA) but exhibited higher transcript levels of ETHYLENE RESPONSE FACTORS (ERFs) and SL and carotenoid related genes, such as TERPENE SYNTHASE (TS), CCD7 and LECITHIN-RETINAL ACYL TRANSFERASE (LRAT). Furthermore, the mutants of M. polymorpha in the SL pathway exhibited increased contents of carotenoid. This unveils a previously unrecognized role for MpD27-1, MpD27-2 and MpCCD7 in controlling release, germination, and growth of gemmae in response to varying light conditions. These discoveries enhance our comprehension of the regulatory functions of SL biosynthesis genes in non-flowering plants.

RevDate: 2024-07-10

Schrecengost A, Rotterová J, Poláková K, et al (2024)

Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts.

The ISME journal pii:7710178 [Epub ahead of print].

Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont ITS region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.

RevDate: 2024-07-11
CmpDate: 2024-07-10

Boanyah GY, Koekemoer LL, Herren JK, et al (2024)

Effect of Microsporidia MB infection on the development and fitness of Anopheles arabiensis under different diet regimes.

Parasites & vectors, 17(1):294.

BACKGROUND: Microsporidia MB (MB) is a naturally occurring symbiont of Anopheles and has recently been identified as having a potential to inhibit the transmission of Plasmodium in mosquitoes. MB intensity is high in mosquito gonads, with no fitness consequences for the mosquito, and is linked to horizontal (sexual) and vertical (transovarial) transmission from one mosquito to another. Maximising MB intensity and transmission is important for maintaining heavily infected mosquito colonies for experiments and ultimately for mosquito releases. We have investigated how diet affects the MB-Anopheles arabiensis symbiosis phenotypes, such as larval development and mortality, adult size and survival, as well as MB intensity in both larvae and adults.

METHODS: F1 larvae of G0 females confirmed to be An. arabiensis and infected with MB were either combined (group lines [GLs]) or reared separately (isofemale lines [IMLs]) depending on the specific experiment. Four diet regimes (all mg/larva/day) were tested on F1 GLs: Tetramin 0.07, Tetramin 0.3, Gocat 0.3 and Cerelac 0.3. GLs reared on Tetramin 0.3 mg/larva/day were then fed either a 1% or 6% glucose diet to determine adult survival. Larvae of IMLs were fed Tetramin 0.07 mg and Tetramin 0.3 mg for larval experiments. The mosquitoes in the adult experiments with IMLs were reared on 1% or 6% glucose.

RESULTS: Amongst the four larval diet regimes tested on An. arabiensis development in the presence of MB, the fastest larval development highest adult emergence, largest body size of mosquitoes, highest prevalence and highest density of MB occurred in those fed Tetramin 0.3 mg/larva/day. Although adult MB-positive mosquitoes fed on 6% glucose survived longer than MB-negative mosquitoes, there was no such effect for those fed on the 1% glucose diet. Development time, wing length and adult survival were not significantly different between MB-infected and uninfected An. arabiensis fed on the Tetramin 0.07 mg/larva/day diet, demonstrating that the MB-conferred fitness advantage was diet-dependent.

CONCLUSIONS: Microsporidia MB does not adversely impact the development and fitness of An. arabiensis, even under limited dietary conditions. The diet regime of Tetramin 0.3 mg/larva/day + 6% glucose for adults is the superior diet for the mass rearing of MB-infected An. arabiensis mosquitoes. These results are important for rearing MB-infected An. arabiensis in the laboratory for experiments and the mass rearing required for field releases.

RevDate: 2024-07-09

Hamada R, Yonezawa A, Matsumoto K, et al (2024)

BTB and CNC homology 1 deficiency disrupts intestinal IgA secretion through regulation of polymeric immunoglobulin receptor expression.

American journal of physiology. Gastrointestinal and liver physiology [Epub ahead of print].

Immunoglobulin A (IgA)-mediated mucosal immunity is important for the host because it contributes to reducing infection risk and to establishing host-microbe symbiosis. BTB and CNC homology 1 (Bach1) is a transcriptional repressor with physiological and pathophysiological functions that are of particular interest for their relation to gastrointestinal diseases. However, Bach1 effects on IgA-mediated mucosal immunity remain unknown. For this study using Bach1-deficient (Bach1[-/-]) mice, we investigated the function of Bach1 in IgA-mediated mucosal immunity. Intestinal mucosa, feces, and plasma IgA were examined using immunosorbent assay. After cell suspensions were prepared from Peyer's patches and colonic lamina propria, they were examined using flow cytometry. The expression level of polymeric immunoglobulin receptor (pIgR), which plays an important role in the transepithelial transport of IgA, was evaluated using Western blotting, quantitative real-time PCR, and immunohistochemistry. Although no changes in the proportions of IgA-producing cells were observed, the amounts of IgA in the intestinal mucosa were increased in Bach1[-/-] mice. Furthermore, plasma IgA was increased in Bach1[-/-] mice, but fecal IgA was decreased, indicating that Bach1[-/-] mice have abnormal secretion of IgA into the intestinal lumen. In fact, Bach1 deficiency reduced pIgR expression in colonic mucosa at both the protein and mRNA levels. In the human intestinal epithelial cell line LS174T, suppression of Bach1 reduced pIgR mRNA stability. In contrast, overexpression of Bach1 increased pIgR mRNA stability. These results demonstrate that Bach1 deficiency causes abnormal secretion of IgA into the intestinal lumen via suppression of pIgR expression.

RevDate: 2024-07-09
CmpDate: 2024-07-09

Probst RS, Longino JT, MG Branstetter (2024)

Evolutionary déjà vu? A case of convergent evolution in an ant-plant association.

Proceedings. Biological sciences, 291(2026):20241214.

Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here, we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, Myrmelachista species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within Myrmelachista are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstructions, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.

RevDate: 2024-07-09
CmpDate: 2024-07-09

Garschall K, Pascual-Carreras E, García-Pascual B, et al (2024)

The cellular basis of feeding-dependent body size plasticity in sea anemones.

Development (Cambridge, England), 151(20):.

Many animals share a lifelong capacity to adapt their growth rates and body sizes to changing environmental food supplies. However, the cellular and molecular basis underlying this plasticity remains only poorly understood. We therefore studied how the sea anemones Nematostella vectensis and Aiptasia (Exaiptasia pallida) respond to feeding and starvation. Combining quantifications of body size and cell numbers with mathematical modelling, we observed that growth and shrinkage rates in Nematostella are exponential, stereotypic and accompanied by dramatic changes in cell numbers. Notably, shrinkage rates, but not growth rates, are independent of body size. In the facultatively symbiotic Aiptasia, we show that growth and cell proliferation rates are dependent on the symbiotic state. On a cellular level, we found that >7% of all cells in Nematostella juveniles reversibly shift between S/G2/M and G1/G0 cell cycle phases when fed or starved, respectively. Furthermore, we demonstrate that polyp growth and cell proliferation are dependent on TOR signalling during feeding. Altogether, we provide a benchmark and resource for further investigating the nutritional regulation of body plasticity on multiple scales using the genetic toolkit available for Nematostella.

RevDate: 2024-07-11
CmpDate: 2024-07-09

Chávez-González JD, Flores-Núñez VM, Merino-Espinoza IU, et al (2024)

Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought.

Environmental microbiology reports, 16(4):e13300.

Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.

RevDate: 2024-07-10

Anderson MD, Taylor DL, Olson K, et al (2024)

Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska.

Ecology and evolution, 14(7):e11458.

In root nodule symbioses (RNS) between nitrogen (N)-fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.

RevDate: 2024-07-08
CmpDate: 2024-07-09

Li X, Liu Q, Gao Y, et al (2024)

Effects of a co-bacterial agent on the growth, disease control, and quality of ginseng based on rhizosphere microbial diversity.

BMC plant biology, 24(1):647.

BACKGROUND: The ginseng endophyte Paenibacillus polymyxa Pp-7250 (Pp-7250) has multifaceted roles such as preventing ginseng diseases, promoting growth, increasing ginsenoside accumulation, and degrading pesticide residues, however, these effects still have room for improvements. Composite fungicides are an effective means to improve the biocontrol effect of fungicides, but the effect of Pp-7250 in combination with its symbiotic bacteria on ginseng needs to be further investigated, and its mechanism of action has not been elucidated. In this study, a series of experiments was conducted to elucidate the effect of Paenibacillus polymyxa and Bacillus cereus co-bacterial agent on the yield and quality of understory ginseng, and to investigate their mechanism of action.

RESULTS: The results indicated that P. polymyxa and B. cereus co-bacterial agent (PB) treatment improved ginseng yield, ginsenoside accumulation, disease prevention, and pesticide degradation. The mechanism is that PB treatment increased the abundance of beneficial microorganisms, including Rhodanobacter, Pseudolabrys, Gemmatimonas, Bacillus, Paenibacillus, Cortinarius, Russula, Paecilomyces, and Trechispora, and decreased the abundance of pathogenic microorganisms, including Ellin6067, Acidibacter, Fusarium, Tetracladium, Alternaria, and Ilyonectria in ginseng rhizosphere soil. PB co-bacterial agents enhanced the function of microbial metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of antibiotics, biosynthesis of amino acids, carbon fixation pathways in prokaryotes, DNA replication, and terpenoid backbone biosynthesis, and decreased the function of microbial plant pathogens and animal pathogens.

CONCLUSION: The combination of P. polymyxa and B. cereus may be a potential biocontrol agent to promote the resistance of ginseng to disease and improve the yield, quality, and pesticide degradation.

RevDate: 2024-07-08

Scheifler M, Wilhelm L, B Visser (2024)

Lipid Metabolism in Parasitoids and Parasitized Hosts.

Advances in experimental medicine and biology [Epub ahead of print].

Parasitoids have an exceptional lifestyle where juvenile development is spent on or in a single host insect, but the adults are free-living. Unlike parasites, parasitoids kill the host. How parasitoids use such a limiting resource, particularly lipids, can affect chances to survive and reproduce. In part 1, we describe the parasitoid lifestyle, including typical developmental strategies. Lipid metabolism in parasitoids has been of interest to researchers since the 1960s and continues to fascinate ecologists, evolutionists, physiologists, and entomologists alike. One reason of this interest is that the majority of parasitoids do not accumulate triacylglycerols as adults. Early research revealed that some parasitoid larvae mimic the fatty acid composition of the host, which may result from a lack of de novo triacylglycerol synthesis. More recent work has focused on the evolution of lack of adult triacylglycerol accumulation and consequences for life history traits. In part 2 of this chapter, we discuss research efforts on lipid metabolism in parasitoids from the 1960s onwards. Parasitoids are also master manipulators of host physiology, including lipid metabolism, having evolved a range of mechanisms to affect the release, synthesis, transport, and take-up of lipids from the host. We lay out the effects of parasitism on host physiology in part 3 of this chapter.

RevDate: 2024-07-08

Ogawa M, Matsutani M, Katayama T, et al (2024)

Discovery of a novel spotted fever group Rickettsia, "Candidatus Rickettsia kedanie," in unfed larval chigger mites, Leptotrombidium scutellare.

Microbiology and immunology [Epub ahead of print].

Spotted fever group (SFG) rickettsia, the causative agent of SFG rickettsiosis, is predominantly carried by ticks, whereas Orientia tsutusgamushi, the causative agent of scrub typhus, is primarily transmitted by chigger mites in Japan. In this study, we attempted to isolate intracellular eubacteria from Leptotrombidium scutellare, a major vector of O. tsutsugamushi; moreover, we isolated an SFG rickettsia using a mosquito-derived cell line. Draft genome sequences of this unique isolate, by applying criteria for species delimitation, classified this isolate as a novel strain, proposed as "Rickettsia kedanie." Further genetic analysis identified conserved virulence factors, and the isolate successfully propagated in mammalian cells, suggesting its ability to cause diseases in humans. The presence of SFG rickettsia in unfed larvae implies potential dual-pathogen carriage and reflects a symbiotic relationship similar to that between the mites and O. tsutsugamushi, indicating possibility of its transovarial transmission from female adults. Furthermore, conserved genomic similarity of the novel isolate to known SFG rickettsia suggests potential multiple hosts, including chiggers and ticks. In the natural environment, ticks, chigger mites, and wild animals may carry new isolates, complicating the infection cycle and increasing the transmission risks to humans. This discovery challenges the conventional association of SFG rickettsia with ticks, emphasizing its implications for research and disease control. However, this study was confined to a particular species of chigger mites and geographic area, underscoring the necessity for additional studies to comprehend the ecological dynamics, host interactions, and health implications linked to this newly identified SFG rickettsia.

RevDate: 2024-07-08

Schaus SR, Vasconcelos Pereira G, Luis AS, et al (2024)

Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron.

mBio [Epub ahead of print].

Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques-a known mucin degrader that has been implicated in inflammatory bowel diseases (IBDs)-degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong α-L-fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which might contribute to its association with IBD.IMPORTANCEAn important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade the various components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate species associated with bacterial mucus damage and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another species of gut bacteria, Bacteroides thetaiotaomicron. Our findings underscore the importance of understanding mucin degradation mechanisms in different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately affect mucus damage and could therefore be key players in effects that result from reductions in mucus integrity.

RevDate: 2024-07-09

Kalani M, A Anjankar (2024)

Revolutionizing Neurology: The Role of Artificial Intelligence in Advancing Diagnosis and Treatment.

Cureus, 16(6):e61706.

Artificial intelligence (AI) has emerged as a powerful tool in the field of neurology, significantly impacting the diagnosis and treatment of neurological disorders. Recent technological breakthroughs have given us access to a plethora of information relevant to many aspects of neurology. Neuroscience and AI share a long history of collaboration. Along with great potential, we encounter obstacles relating to data quality, ethics, and inherent difficulty in applying data science in healthcare. Neurological disorders pose intricate challenges due to their complex manifestations and variability. Automating image interpretation tasks, AI algorithms accurately identify brain structures and detect abnormalities. This accelerates diagnosis and reduces the workload on medical professionals. Treatment optimization benefits from AI simulations that model different scenarios and predict outcomes. These AI systems can currently perform many of the sophisticated perceptual and cognitive capacities of biological systems, such as object identification and decision making. Furthermore, AI is rapidly being used as a tool in neuroscience research, altering our understanding of brain functioning. It has the ability to revolutionize healthcare as we know it into a system in which humans and robots collaborate to deliver better care for our patients. Image analysis activities such as recognizing particular brain regions, calculating changes in brain volume over time, and detecting abnormalities in brain scans can be automated by AI systems. This lessens the strain on radiologists and neurologists while improving diagnostic accuracy and efficiency. It is now obvious that cutting-edge artificial intelligence models combined with high-quality clinical data will lead to enhanced prognostic and diagnostic models in neurological illness, permitting expert-level clinical decision aids across healthcare settings. In conclusion, AI's integration into neurology has revolutionized diagnosis, treatment, and research. As AI technologies advance, they promise to unravel the complexities of neurological disorders further, leading to improved patient care and quality of life. The symbiosis of AI and neurology offers a glimpse into a future where innovation and compassion converge to reshape neurological healthcare. This abstract provides a concise overview of the role of AI in neurology and its transformative potential.

RevDate: 2024-07-09

Guo S, Xia L, Xia D, et al (2024)

Enhancing plant resilience: arbuscular mycorrhizal fungi's role in alleviating drought stress in vegetation concrete.

Frontiers in plant science, 15:1401050.

INTRODUCTION: Drought stress usually inhibits plant growth, which may increase the difficulty of greening slopes.

METHODS: In this study, we systematically investigated the effects of arbuscular mycorrhizal (AM) fungi on the growth and drought tolerance of two plant species, Festuca elata and Cassia glauca, in a vegetation concrete environment by exogenously inoculating AM fungi and setting three drought levels: well water, moderate drought and severe drought. The results showed that plant growth was significantly inhibited under drought stress; however, AM fungi inoculation significantly promoted plant height, root length, and above- and belowground biomass in these two plant species.

RESULTS: Compared with, those in the CK treatment, the greatest increases in the net photosynthesis rate, stomatal conductance and transpiration rate in the AM treatment group were 36.72%, 210.08%, and 66.41%, respectively. Moreover, inoculation with AM fungi increased plant superoxide dismutase and catalase activities by 4.70-150.73% and 9.10-95.70%, respectively, and reduced leaf malondialdehyde content by 2.79-55.01%, which alleviated the damage caused by oxidative stress. These effects alleviated the damage caused by oxidative stress and increased the content of soluble sugars and soluble proteins in plant leaves by 1.52-65.44% and 4.67-97.54%, respectively, which further increased the drought adaptability of plants. However, inoculation with AM fungi had different effects on different plants.

CONCLUSION: In summary, this study demonstrated that the inoculation of AM fungi in vegetation concrete environments can significantly increase plant growth and drought tolerance. The plants that formed a symbiotic structure with AM fungi had a larger root uptake area, greater water uptake capacity, and greater photosynthesis and gas exchange efficiency. In addition, AM fungi inoculation further increased the drought adaptability of the plants by increasing their antioxidant enzyme activity and regulating their metabolite content. These findings are highly important for promoting plant growth and increasing drought tolerance under drought conditions, especially for potential practical applications in areas such as slope protection, and provide useful references for future ecological engineering and sustainable development.

RevDate: 2024-07-08

Zhang J, Yang S, KU Rehman (2024)

Editorial: Gut microbiome in black soldier fly (Hermetia illucens L.) larvae: symbiosis, function, and application.

Frontiers in microbiology, 15:1441577.

RevDate: 2024-07-08
CmpDate: 2024-07-08

Qi J, Mao Y, Cui J, et al (2024)

The role of strigolactones in resistance to environmental stress in plants.

Physiologia plantarum, 176(4):e14419.

Abiotic stress impairs plant growth and development, thereby causing low yield and inferior quality of crops. Increasing studies reported that strigolactones (SL) are plant hormones that enhance plant stress resistance by regulating plant physiological processes and gene expressions. In this review, we introduce the response and regulatory role of SL in salt, drought, light, heat, cold and cadmium stresses in plants. This review also discusses how SL alleviate the damage of abiotic stress in plants, furthermore, introducing the mechanisms of SL enhancing plant stress resistance at the genetic level. Under abiotic stress, the exogenous SL analog GR24 can induce the biosynthesis of SL in plants, and endogenous SL can alleviate the damage caused by abiotic stress. SL enhanced the stress resistance of plants by protecting photosynthesis, enhancing the antioxidant capacity of plants and promoting the symbiosis between plants and arbuscular mycorrhiza (AM). SL interact with abscisic acid (ABA), salicylic acid (SA), auxin, cytokinin (CK), jasmonic acid (JA), hydrogen peroxide (H2O2) and other signal molecules to jointly regulate plant stress resistance. Lastly, both the importance of SL and their challenges for future work are outlined in order to further elucidate the specific mechanisms underlying the roles of SL in plant responses to abiotic stress.

RevDate: 2024-07-08

Yu B, Zhou C, Wang Z, et al (2024)

Maize zinc uptake is influenced by arbuscular mycorrhizal symbiosis under various soil phosphorus availabilities.

The New phytologist [Epub ahead of print].

The antagonistic interplay between phosphorus (P) and zinc (Zn) in plants is well established. However, the molecular mechanisms mediating those interactions as influenced by arbuscular mycorrhizal (AM) symbiosis remain unclear. We investigated Zn concentrations, root AM symbiosis, and transcriptome profiles of maize roots grown under field conditions upon different P levels. We also validated genotype-dependent P-Zn uptake in selected genotypes from a MAGIC population and conducted mycorrhizal inoculation experiments using mycorrhizal-defective mutant pht1;6 to elucidate the significance of AM symbiosis in P-Zn antagonism. Finally, we assessed how P supply affects Zn transporters and Zn uptake in extraradical hyphae within a three-compartment system. Elevated P levels led to a significant reduction in maize Zn concentration across the population, correlating with a marked decline in AM symbiosis, thus elucidating the P-Zn antagonism. We also identified ZmPht1;6 is crucial for AM symbiosis and confirmed that P-Zn antagonistic uptake is dependent on AM symbiosis. Moreover, we found that high P suppressed the expression of the fungal RiZRT1 and RiZnT1 genes, potentially impacting hyphal Zn uptake. We conclude that high P exerts systemic regulation over root and AM hyphae-mediated Zn uptake in maize. These findings hold implications for breeding Zn deficiency-tolerant maize varieties.

RevDate: 2024-07-09
CmpDate: 2024-07-07

Marulanda-Gomez AM, Ribes M, Franzenburg S, et al (2024)

Transcriptomic responses of Mediterranean sponges upon encounter with symbiont microbial consortia.

BMC genomics, 25(1):674.

BACKGROUND: Sponges (phylum Porifera) constantly interact with microbes. They graze on microbes from the water column by filter-feeding and they harbor symbiotic partners within their bodies. In experimental setups, sponges take up symbionts at lower rates compared with seawater microbes. This suggests that sponges have the capacity to differentiate between microbes and preferentially graze in non-symbiotic microbes, although the underlying mechanisms of discrimination are still poorly understood. Genomic studies showed that, compared to other animal groups, sponges present an extended repertoire of immune receptors, in particular NLRs, SRCRs, and GPCRs, and a handful of experiments showed that sponges regulate the expression of these receptors upon encounter with microbial elicitors. We hypothesize that sponges may rely on differential expression of their diverse repertoire of poriferan immune receptors to sense different microbial consortia while filter-feeding. To test this, we characterized the transcriptomic response of two sponge species, Aplysina aerophoba and Dysidea avara, upon incubation with microbial consortia extracted from A. aerophoba in comparison with incubation with seawater microbes. The sponges were sampled after 1 h, 3 h, and 5 h for RNA-Seq differential gene expression analysis.

RESULTS: D. avara incubated with A. aerophoba-symbionts regulated the expression of genes related to immunity, ubiquitination, and signaling. Within the set of differentially-expressed immune genes we identified different families of Nucleotide Oligomerization Domain (NOD)-Like Receptors (NLRs). These results represent the first experimental evidence that different types of NLRs are involved in microbial discrimination in a sponge. In contrast, the transcriptomic response of A. aerophoba to its own symbionts involved comparatively fewer genes and lacked genes encoding for immune receptors.

CONCLUSION: Our work suggests that: (i) the transcriptomic response of sponges upon microbial exposure may imply "fine-tuning" of baseline gene expression as a result of their interaction with microbes, (ii) the differential response of sponges to microbial encounters varied between the species, probably due to species-specific characteristics or related to host's traits, and (iii) immune receptors belonging to different families of NLR-like genes played a role in the differential response to microbes, whether symbionts or food bacteria. The regulation of these receptors in sponges provides further evidence of the potential role of NLRs in invertebrate host-microbe interactions. The study of sponge responses to microbes exemplifies how investigating different animal groups broadens our knowledge of the evolution of immune specificity and symbiosis.

RevDate: 2024-07-09
CmpDate: 2024-07-06

Bhat A, Sharma R, Desigan K, et al (2024)

Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria.

BMC microbiology, 24(1):247.

BACKGROUND: Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg.

RESULTS: Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg.

CONCLUSIONS: Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.

RevDate: 2024-07-09

Jacobs J, Nakamoto A, Mastoras M, et al (2024)

Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing.

Research square.

Wolbachia is an obligate intracellular α-proteobacterium which commonly infects arthropods and filarial nematodes. Different strains of Wolbachia are capable of a wide range of regulatory manipulations in many hosts and modulate host cellular differentiation to influence host reproduction. The genetic basis for the majority of these phenotypes is unknown. The wWil strain from the neotropical fruit fly, Drosophila willistoni, exhibits a remarkably high affinity for host germline-derived cells relative to the soma. This trait could be leveraged for understanding how Wolbachia influences the host germline and for controlling host populations in the field. To further the use of this strain in biological and biomedical research, we sequenced the genome of the wWil strain isolated from host cell culture cells. Here, we present the first high quality nanopore assembly of wWil, the Wolbachia endosymbiont of D. willistoni. Our assembly resulted in a circular genome of 1.27 Mb with a BUSCO completeness score of 99.7%. Consistent with other insect-associated Wolbachia strains, comparative genomic analysis revealed that wWil has a highly mosaic genome relative to the closely related wMel strain from Drosophila melanogaster.

RevDate: 2024-07-06

Prosdocimi F, ST Farias (2024)

Major evolutionary transitions before cells: a journey from molecules to organisms.

Progress in biophysics and molecular biology pii:S0079-6107(24)00059-2 [Epub ahead of print].

Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.

RevDate: 2024-07-08
CmpDate: 2024-07-06

Alghamdi AK, Parween S, Hirt H, et al (2024)

Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina.

BMC genomics, 25(1):672.

The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium's adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.

RevDate: 2024-07-08

Zhou JR, Li XQ, Yu X, et al (2024)

Exploring the ecological security evaluation of water resources in the Yangtze River Basin under the background of ecological sustainable development.

Scientific reports, 14(1):15475.

The Yangtze River (hereafter referred to as the YZR), the largest river in China, is of paramount importance for ensuring water resource security. The Yangtze River Basin (hereafter referred to as the YRB) is one of the most densely populated areas in China, and complex human activities have a significant impact on the ecological security of water resources. Therefore, this paper employs theories related to ecological population evolution and the Driving Force-Pressure-State-Impact-Response (DPSIR) model to construct an indicator system for the ecological security of water resources in the YRB. The report evaluates the ecological security status of water resources in each province of the YRB from 2010 to 2019, clarifies the development trend of its water resource ecological security, and proposes corresponding strategies for regional ecological security and coordinated economic development. According to the results of the ecological population evolution competition model, the overall indicator of the ecological security of water resources in the YRB continues to improve, with the safety level increasing annually. Maintaining sound management of water resources in the YRB is crucial for sustainable socioeconomic development. To further promote the ecological security of water resources in the YRB and the coordinated development of the regional economy, this paper proposes policy suggestions such as promoting the continuous advancement of sustainable development projects, actively adjusting industrial structure, continuously enhancing public environmental awareness, and actively participating in international ecological construction and seeking cooperation among multiple departments.

RevDate: 2024-07-08
CmpDate: 2024-07-05

Wuitchik DM, Aichelman HE, Atherton KF, et al (2024)

Photosymbiosis reduces the environmental stress response under a heat challenge in a facultatively symbiotic coral.

Scientific reports, 14(1):15484.

The symbiosis between corals and dinoflagellates of the family Symbiodiniaceae is sensitive to environmental stress. The oxidative bleaching hypothesis posits that extreme temperatures lead to accumulation of photobiont-derived reactive oxygen species ROS, which exacerbates the coral environmental stress response (ESR). To understand how photosymbiosis modulates coral ESRs, these responses must be explored in hosts in and out of symbiosis. We leveraged the facultatively symbiotic coral Astrangia poculata, which offers an opportunity to uncouple the ESR across its two symbiotic phenotypes (brown, white). Colonies of both symbiotic phenotypes were exposed to three temperature treatments for 15 days: (i) control (static 18 °C), (ii) heat challenge (increasing from 18 to 30 °C), and (iii) cold challenge (decreasing from 18 to 4 °C) after which host gene expression was profiled. Cold challenged corals elicited widespread differential expression, however, there were no differences between symbiotic phenotypes. In contrast, brown colonies exhibited greater gene expression plasticity under heat challenge, including enrichment of cell cycle pathways involved in controlling photobiont growth. While this plasticity was greater, the genes driving this plasticity were not associated with an amplified environmental stress response (ESR) and instead showed patterns of a dampened ESR under heat challenge. This provides nuance to the oxidative bleaching hypothesis and suggests that, at least during the early onset of bleaching, photobionts reduce the host's ESR under elevated temperatures in A. poculata.

RevDate: 2024-07-07

Sharma V, Sharma DP, R Salwan (2024)

Surviving the stress: Understanding the molecular basis of plant adaptations and uncovering the role of mycorrhizal association in plant abiotic stresses.

Microbial pathogenesis, 193:106772 pii:S0882-4010(24)00239-0 [Epub ahead of print].

Environmental stresses severely impair plant growth, resulting in significant crop yield and quality loss. Among various abiotic factors, salt and drought stresses are one of the major factors that affect the nutrients and water uptake by the plants, hence ultimately various physiological aspects of the plants that compromises crop yield. Continuous efforts have been made to investigate, dissect and improve plant adaptations at the molecular level in response to drought and salinity stresses. In this context, the plant beneficial microbiome presents in the rhizosphere, endosphere, and phyllosphere, also referred as second genomes of the plant is well known for its roles in plant adaptations. Exploration of beneficial interaction of fungi with host plants known as mycorrhizal association is one such special interaction that can facilitates the host plants adaptations. Mycorrhiza assist in alleviating the salinity and drought stresses of plants via redistributing the ion imbalance through translocation to different parts of the plants, as well as triggering oxidative machinery. Mycorrhiza association also regulates the level of various plant growth regulators, osmolytes and assists in acquiring minerals that are helpful in plant's adaptation against extreme environmental stresses. The current review examines the role of various plant growth regulators and plants' antioxidative systems, followed by mycorrhizal association during drought and salt stresses.

RevDate: 2024-07-05

Lau KJX, Selvaraj P, Muralishankar V, et al (2024)

Draft genome sequence of Penicillium citrinum B9, a plant growth-promoting symbiont from barley rhizosphere.

Microbiology resource announcements [Epub ahead of print].

Penicillium citrinum strain B9 is a plant growth-promoting fungus isolated from Barley (Hordeum vulgare) rhizosphere. We report the first draft genome of P. citrinum B9 assembled using single-molecule real-time sequencing and Illumina reads. The assembled genome spans 31.3 Mb comprising nine contigs and 10,106 protein-encoding genes.

RevDate: 2024-07-06

Jung P, Briegel-Williams L, Büdel B, et al (2024)

The underestimated fraction: diversity, challenges and novel insights into unicellular cyanobionts of lichens.

ISME communications, 4(1):ycae069.

Lichens are remarkable and classic examples of symbiotic organisms that have fascinated scientists for centuries. Yet, it has only been for a couple of decades that significant advances have focused on the diversity of their green algal and/or cyanobacterial photobionts. Cyanolichens, which contain cyanobacteria as their photosynthetic partner, include up to 10% of all known lichens and, as such, studies on their cyanobionts are much rarer compared to their green algal counterparts. For the unicellular cyanobionts, i.e. cyanobacteria that do not form filaments, these studies are even scarcer. Nonetheless, these currently include at least 10 different genera in the cosmopolitan lichen order Lichinales. An international consortium (International Network of CyanoBionts; INCb) will tackle this lack of knowledge. In this article, we discuss the status of current unicellular cyanobiont research, compare the taxonomic resolution of photobionts from cyanolichens with those of green algal lichens (chlorolichens), and give a roadmap of research on how to recondition the underestimated fraction of symbiotic unicellular cyanobacteria in lichens.

RevDate: 2024-07-05

Romero-Munar A, Muñoz-Carrasco M, Balestrini R, et al (2024)

Differential root and cell regulation of maize aquaporins by the arbuscular mycorrhizal symbiosis highlights its role in plant water relations.

Plant, cell & environment [Epub ahead of print].

This study aims to elucidate if the regulation of plant aquaporins by the arbuscular mycorrhizal (AM) symbiosis occurs only in roots or cells colonized by the fungus or at whole root system. Maize plants were cultivated in a split-root system, with half of the root system inoculated with the AM fungus and the other half uninoculated. Plant growth and hydraulic parameters were measured and aquaporin gene expression was determined in each root fraction and in microdissected cells. Under well-watered conditions, the non-colonized root fractions of AM plants grew more than the colonized root fraction. Total osmotic and hydrostatic root hydraulic conductivities (Lo and Lpr) were higher in AM plants than in non-mycorrhizal plants. The expression of most maize aquaporin genes analysed was different in the mycorrhizal root fraction than in the non-mycorrhizal root fraction of AM plants. At the cellular level, differential aquaporin expression in AM-colonized cells and in uncolonized cells was also observed. Results indicate the existence of both, local and systemic regulation of plant aquaporins by the AM symbiosis and suggest that such regulation is related to the availability of water taken up by fungal hyphae in each root fraction and to the plant need of water mobilization.

RevDate: 2024-07-07
CmpDate: 2024-07-05

Babajanyan SG, Garushyants SK, Wolf YI, et al (2024)

Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.

BMC biology, 22(1):148.

BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.

RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.

CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.

RevDate: 2024-07-04

Wang T, Chen Q, Liang Q, et al (2024)

Bacillus suppresses nitrogen efficiency of soybean-rhizobium symbiosis through regulation of nitrogen-related transcriptional and microbial patterns.

Plant, cell & environment [Epub ahead of print].

The regulation of legume-rhizobia symbiosis by microorganisms has obtained considerable interest in recent research, particularly in the common rhizobacteria Bacillus. However, few studies have provided detailed explanations regarding the regulatory mechanisms involved. Here, we investigated the effects of Bacillus (Bac.B) on Bradyrhizobium-soybean (Glycine max) symbiosis and elucidated the underlying ecological mechanisms. We found that two Bradyrhizobium strains (i.e. Bra.Q2 and Bra.D) isolated from nodules significantly promoted nitrogen (N) efficiency of soybean via facilitating nodule formation, thereby enhanced plant growth and yield. However, the intrusion of Bac.B caused a reverse shift in the synergistic efficiency of N2 fixation in the soybean-Bradyrhizobium symbiosis. Biofilm formation and naringenin may be importantin suppression of Bra.Q2 growth regulated by Bac.B. In addition, transcriptome and microbiome analyses revealed that Bra.Q2 and Bac.B might interact to regulateN transport and assimilation, thus influence the bacterial composition related to plant N nutrition in nodules. Also, the metabolisms of secondary metabolites and hormones associated with plant-microbe interaction and growth regulation were modulated by Bra.Q2 and Bac.B coinoculation. Collectively, we demonstrate that Bacillus negatively affects Bradyrhizobium-soybean symbiosis and modulate microbial interactions in the nodule. Our findings highlight a novel Bacillus-based regulation to improve N efficiency and sustainable agricultural development.

RevDate: 2024-07-05

Zhang B, Yang W, He Q, et al (2024)

Analysis of differential effects of host plants on the gut microbes of Rhoptroceros cyatheae.

Frontiers in microbiology, 15:1392586.

As an indispensable part of insects, intestinal symbiotic bacteria play a vital role in the growth and development of insects and their adaptability. Rhoptroceros cyatheae, the main pest of the relict plant Alsophila spinulosa, poses a serious threat to the development of the A. spinulosa population. In the present study, 16S rDNA and internal transcribed spacer high-throughput sequencing techniques were used to analyze the structure of intestinal microbes and the diversity of the insect feeding on two different plants, as well as the similarities between the intestinal microorganisms of R. cyatheae. The dominant bacteria of leaf endophytes were also compared based on the sequencing data. The results showed that Proteobacteria, Firmicutes, and Actinobacteria were the dominant phyla of intestinal bacteria, and Ascomycota was the dominant phylum of intestinal fungi. Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Methylobacterium-Methylorubrum, and Enterococcus were the dominant genera in the intestine of R. cyatheae feeding on two plants, and the relative abundance was significantly different between the two groups. Candida was the common dominant genus of intestinal fungi in the two groups, and no significant difference was observed in its abundance between the two groups. This showed that compared with the intestinal fungi of R. cyatheae, the abundance of the intestinal bacteria was greatly affected by food. The common core microbiota between the microorganisms in A. spinulosa leaves and the insect gut indicated the presence of a microbial exchange between the two. The network correlation diagram showed that the gut microbes of R. cyatheae feeding on Gymnosphaera metteniana were more closely related to each other, which could help the host to better cope with the adverse external environment. This study provides a theoretical basis for the adaptation mechanism of R. cyatheae and a new direction for the effective prevention and control of R. cyatheae.

RevDate: 2024-07-05

Chen Z, X Dai (2024)

Utilizing AI and IoT technologies for identifying risk factors in sports.

Heliyon, 10(11):e32477.

A dynamic cooperation is poised to redefine the limits of athlete safety and performance optimization in the dynamic field of sports science. A new age in sports analysis is promised by the combination of artificial intelligence (AI) and the internet of things (IoT), one in which data-driven insights not only improve our comprehension of athletic performance but also aid to reduce hazards. This academic work explores the complex interactions between AI and IoT in the context of sports. The IoT and AI integration appear to be a strong mix that has the potential to redefine the standards for athlete safety and performance improvement. This study explores the complex interactions between AI and IoT in the field of sports, emphasizing their combined potential for identifying risk factors in a variety of fields. There is a chance to proactively solve sports-related difficulties by utilizing the data-driven capabilities of IoT and the analytical power of AI, opening the door for better informed tactics and decision-making. Through an exploration of this symbiotic relationship, this paper seeks to underline the transformative potential of these technologies in fostering a safer and more performance-oriented sports environment.

RevDate: 2024-07-05

Kumari A, Choudhary JS, Thakur AK, et al (2024)

Substantially altered bacterial diversity associated with developmental stages of litchi stink bug, Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae).

Heliyon, 10(11):e32384.

The mutualistic symbiotic relationship between insects and bacteria greatly influences the growth and development of host insects. Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae), also referred to as the litchi stink bug, has recently been established as an important insect pest of Litchi chinensis Sonn. and causes substantial yield loss in India. To design effective and environmentally safe management strategies, an understanding of the diversity and functions of microbiota harbored across the development stages is very important. The assessment of the diversity of development-associated bacteria in T. javanica and their predicted functions was conducted using 16S rRNA gene sequences obtained by the Illumina MiSeq technology. The result showed that taxonomic analysis of associated bacteria in different developmental stages includes a total of 46 phyla, encompassing 139 classes, 271 orders, 474 families, and 893 genera of bacteria. All developmental stages of T. javanica shared a total of 42.82 percent of operational taxonomic units (OTUs), with a 97 % similarity threshold. Alpha diversity indices showed maximum species richness in the egg and adult stages. The phyla Proteobacteria followed by Firmicutes, Bacteriodetes, and Actinobacteria, exhibited the highest levels of abundance across all the developmental stages of T. javanica. Microbiota were most different between the egg and the 4th nymphal stage (χ2 = 711.67) and least different between the 2nd and 4th nymphal instars (χ2 = 44.45). The predicted functions of the microbiota associated with T. javanica are mainly involved in amino acid metabolism, cell motility, cellular processes and signaling, glycan biosynthesis and metabolism, lipid metabolism, and membrane transport. The present study documentation and information on symbiotic bacteria across T. javanica life stages will prompt the development of novel biological management strategies.

RevDate: 2024-07-04
CmpDate: 2024-07-03

Gore MN, Drozd ME, RS Patil (2024)

Anemia Prevalence and Socioeconomic Status among Adolescent Girls in Rural Western India: A Cross-Sectional Study.

Ethiopian journal of health sciences, 34(1):57-64.

BACKGROUND: Anemia poses a significant challenge among Indian adolescent girls due to their heightened vulnerability, resulting from increased micronutrient requirements, rapid physical growth, menstrual blood loss, inadequate nutrition, and socioeconomic disparities. This study sought to evaluate the prevalence of anemia, along with socioeconomic and nutritional statuses among adolescent girls attending rural public schools in Pune, India.

METHODS: A sample of 400 girls was selected from 22 villages through Symbiosis International University. Hemoglobin levels were assessed using the HemoCue 201 system, while standardized protocols were employed for height, weight, and BMI-for-age measurements. Socioeconomic status was determined using the Kuppuswamy scale.

RESULTS: The findings revealed an overall anemia prevalence of (42.75%), comprising severe (2.5%), moderate (21%) and mild (20.25%) cases. Additionally, a substantial proportion (74.6%) of girls were classified as underweight. Socioeconomic analysis disclosed that 64.25% of families belonged to the lower middle class, and 27% in the upper lower class. Anemia was more prevalent in young adolescent girls (10-14 years) and in the families of adolescents who had low income, were illiterate, unemployed, and belonged to the lower-middle class and upper-lower-class socio-economic status (SES) and did not have a bank account.

CONCLUSION: Anemia was prevalent in adolescent girls and associated with low SES. This study underscores the limitations of relying solely on the distribution of iron and folic acid tablets to combat anemia. A holistic strategy is imperative, encompassing improvements in SES of families (literacy, employment and income), as well as initiatives aimed at enhancing the nutritional status of adolescent girls.

RevDate: 2024-07-03

Kryukov VY, Kosman E, Slepneva I, et al (2024)

Involvement of bacteria in the development of fungal infections in the Colorado potato beetle.

Insect science [Epub ahead of print].

Entomopathogenic fungi may interact with insects' symbiotic bacteria during infection. We hypothesized that topical infection with Beauveria bassiana may alter the microbiota of the Colorado potato beetle (CPB) and that these modifications may alter the course of mycoses. We used a model with two concentrations of conidia: (1) high concentration that causes rapid (acute) pathogenesis with fast mortality followed by bacterial decomposition of insects; (2) lower concentration that leads to prolonged pathogenesis ending in conidiation on cadavers. The fungal infections increased loads of enterobacteria and bacilli on the cuticle surface and in hemolymph and midgut, and the greatest increase was detected during the acute mycosis. By contrast, stronger activation of IMD and JAK-STAT signaling pathways in integuments and fat body was observed during the prolonged mycosis. Relatively stable (nonpathogenic) conditions remained in the midgut during both scenarios of mycosis with slight changes in bacterial communities, the absence of mesh and stat expression, a decrease in reactive oxygen species production, and slight induction of Toll and IMD pathways. Oral administration of antibiotic and predominant CPB bacteria (Enterobacteriaceae, Lactococcus, Pseudomonas) led to minor and mainly antagonistic effects in survival of larvae infected with B. bassiana. We believe that prolonged mycosis is necessary for successful development of the fungus because such pathogenesis allows the host to activate antibacterial reactions. Conversely, after infection with high concentrations of the fungus, the host's resources are insufficient to fully activate antibacterial defenses, and this situation makes successful development of the fungus impossible.

RevDate: 2024-07-05
CmpDate: 2024-07-03

Miranda FM, Azevedo VC, Ramos RJ, et al (2024)

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2.

BMC bioinformatics, 25(1):228.

BACKGROUND: Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi. Hence, an accurate and robust method for ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight into the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them fully explore the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors.

RESULTS: Here we introduce HiTaC, a robust hierarchical machine learning model for accurate ITS classification, which requires a small amount of data for training and can handle imbalanced datasets. HiTaC was thoroughly evaluated with the established TAXXI benchmark and could correctly classify fungal ITS sequences of varying lengths and a range of identity differences between the training and test data. HiTaC outperforms state-of-the-art methods when trained over noisy data, consistently achieving higher F1-score and sensitivity across different taxonomic ranks, improving sensitivity by 6.9 percentage points over top methods in the most noisy dataset available on TAXXI.

CONCLUSIONS: HiTaC is publicly available at the Python package index, BIOCONDA and Docker Hub. It is released under the new BSD license, allowing free use in academia and industry. Source code and documentation, which includes installation and usage instructions, are available at https://gitlab.com/dacs-hpi/hitac .

RevDate: 2024-07-02
CmpDate: 2024-07-02

Das D, PK Panda (2024)

Pseudomonas and aspergillus symbiotic coinfections in a case of chronic obstructive pulmonary disease and diabetes mellitus.

BMJ case reports, 17(7): pii:17/7/e259285.

Coinfection of Pseudomonas and Aspergillus has not been previously reported in patients with chronic obstructive pulmonary disease (COPD). A middle-aged, thinly built woman (Body Mass Index: 18.1 kg/m[2]) who smokes bidi (a type of tobacco) and has a history of exposure to open log fires for cooking, has been suffering from COPD for the last 4 years. She has been taking inhaled betamethasone and tiotropium. Additionally, she had uncontrolled diabetes for a few months. She presented with fever, productive cough, shortness of breath and chest pain for 5 days. She required non-invasive ventilation support for type-2 respiratory failure. Chest X-ray and CT confirmed pneumonia, cavities and abscesses in both lungs. Repeated sputum and bronchoalveolar lavage confirmed coinfections with Pseudomonas aeruginosa and Aspergillus fumigatus, respectively. Along with supportive therapy, she was treated with tablet levofloxacin and injection amikacin for 6 weeks based on culture sensitivity reports, and capsule itraconazole for 6 months. She recovered completely to her baseline COPD and diabetes status. This case study confirms that coinfections can occur in COPD and diabetes, highlighting the need for clinicians to be vigilant for the possibility of such symbiotic coinfections.

RevDate: 2024-07-02

Chen J, Qian L, Ma L, et al (2024)

SymTC: A symbiotic Transformer-CNN net for instance segmentation of lumbar spine MRI.

Computers in biology and medicine, 179:108795 pii:S0010-4825(24)00880-1 [Epub ahead of print].

Intervertebral disc disease, a prevalent ailment, frequently leads to intermittent or persistent low back pain, and diagnosing and assessing of this disease rely on accurate measurement of vertebral bone and intervertebral disc geometries from lumbar MR images. Deep neural network (DNN) models may assist clinicians with more efficient image segmentation of individual instances (discs and vertebrae) of the lumbar spine in an automated way, which is termed as instance image segmentation. In this work, we proposed SymTC, an innovative lumbar spine MR image segmentation model that combines the strengths of Transformer and Convolutional Neural Network (CNN). Specifically, we designed a parallel dual-path architecture to merge CNN layers and Transformer layers, and we integrated a novel position embedding into the self-attention module of Transformer, enhancing the utilization of positional information for more accurate segmentation. To further improve model performance, we introduced a new data synthesis technique to create synthetic yet realistic MR image dataset, named SSMSpine, which is made publicly available. We evaluated our SymTC and the other 16 representative image segmentation models on our private in-house dataset and public SSMSpine dataset, using two metrics, Dice Similarity Coefficient and the 95th percentile Hausdorff Distance. The results indicate that SymTC surpasses the other 16 methods, achieving the highest dice score of 96.169 % for segmenting vertebral bones and intervertebral discs on the SSMSpine dataset. The SymTC code and SSMSpine dataset are publicly available at https://github.com/jiasongchen/SymTC.

RevDate: 2024-07-02

Abdel-Salam M, Hu G, Çelik E, et al (2024)

Chaotic RIME optimization algorithm with adaptive mutualism for feature selection problems.

Computers in biology and medicine, 179:108803 pii:S0010-4825(24)00888-6 [Epub ahead of print].

The RIME optimization algorithm is a newly developed physics-based optimization algorithm used for solving optimization problems. The RIME algorithm proved high-performing in various fields and domains, providing a high-performance solution. Nevertheless, like many swarm-based optimization algorithms, RIME suffers from many limitations, including the exploration-exploitation balance not being well balanced. In addition, the likelihood of falling into local optimal solutions is high, and the convergence speed still needs some work. Hence, there is room for enhancement in the search mechanism so that various search agents can discover new solutions. The authors suggest an adaptive chaotic version of the RIME algorithm named ACRIME, which incorporates four main improvements, including an intelligent population initialization using chaotic maps, a novel adaptive modified Symbiotic Organism Search (SOS) mutualism phase, a novel mixed mutation strategy, and the utilization of restart strategy. The main goal of these improvements is to improve the variety of the population, achieve a better balance between exploration and exploitation, and improve RIME's local and global search abilities. The study assesses the effectiveness of ACRIME by using the standard benchmark functions of the CEC2005 and CEC2019 benchmarks. The proposed ACRIME is also applied as a feature selection to fourteen various datasets to test its applicability to real-world problems. Besides, the ACRIME algorithm is applied to the COVID-19 classification real problem to test its applicability and performance further. The suggested algorithm is compared to other sophisticated classical and advanced metaheuristics, and its performance is assessed using statistical tests such as Wilcoxon rank-sum and Friedman rank tests. The study demonstrates that ACRIME exhibits a high level of competitiveness and often outperforms competing algorithms. It discovers the optimal subset of features, enhancing the accuracy of classification and minimizing the number of features employed. This study primarily focuses on enhancing the equilibrium between exploration and exploitation, extending the scope of local search.

RevDate: 2024-07-02

Siddique A, Al Disi Z, AlGhouti M, et al (2024)

Diversity of hydrocarbon-degrading bacteria in mangroves rhizosphere as an indicator of oil-pollution bioremediation in mangrove forests.

Marine pollution bulletin, 205:116620 pii:S0025-326X(24)00597-6 [Epub ahead of print].

Mangrove ecosystems, characterized by high levels of productivity, are susceptible to anthropogenic activities, notably oil pollution arising from diverse origins including spills, transportation, and industrial effluents. Owing to their role in climate regulation and economic significance, there is a growing interest in developing mangrove conservation strategies. In the Arabian Gulf, mangroves stand as the sole naturally occurring green vegetation due to the region's hot and arid climate. However, they have faced persistent oil pollution for decades. This review focuses on global mangrove distribution, with a specific emphasis on Qatar's mangroves. It highlights the ongoing challenges faced by mangroves, particularly in relation to the oil industry, and the impact of oil pollution on these vital ecosystems. It outlines major oil spill incidents worldwide and the diverse hydrocarbon-degrading bacterial communities within polluted areas, elucidating their potential for bioremediation. The use of symbiotic interactions between mangrove plants and bacteria offers a more sustainable, cost-effective and environmentally friendly alternative. However, the success of these bioremediation strategies depends on a deep understanding of the dynamics of bacterial communities, environmental factors and specific nature of the pollutants.

RevDate: 2024-07-02

Gilhar O, Ben-Navi LR, Olender T, et al (2024)

Multigenerational inheritance drives symbiotic interactions of the bacterium Bacillus subtilis with its plant host.

Microbiological research, 286:127814 pii:S0944-5013(24)00215-5 [Epub ahead of print].

Bacillus subtilis is a beneficial bacterium that supports plant growth and protects plants from bacterial, fungal, and viral infections. Using a simplified system of B. subtilis and Arabidopsis thaliana interactions, we studied the fitness and transcriptome of bacteria detached from the root over generations of growth in LB medium. We found that bacteria previously associated with the root or exposed to its secretions had greater stress tolerance and were more competitive in root colonization than bacteria not previously exposed to the root. Furthermore, our transcriptome results provide evidence that plant secretions induce a microbial stress response and fundamentally alter signaling by the cyclic nucleotide c-di-AMP, a signature maintained by their descendants. The changes in cellular physiology due to exposure to plant exudates were multigenerational, as they allowed not only the bacterial cells that colonized a new plant but also their descendants to have an advance over naive competitors of the same species, while the overall plasticity of gene expression and rapid adaptation were maintained. These changes were hereditary but not permanent. Our work demonstrates a bacterial memory manifested by multigenerational reversible adaptation to plant hosts in the form of activation of the stressosome, which confers an advantage to symbiotic bacteria during competition.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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In this comprehensive history of symbiosis theory--the first to be written--Jan Sapp masterfully traces its development from modest beginnings in the late nineteenth century to its current status as one of the key conceptual frameworks for the life sciences. The symbiotic perspective on evolution, which argues that "higher species" have evolved from a merger of two or more different kinds of organisms living together, is now clearly established with definitive molecular evidence demonstrating that mitochondria and chloroplasts have evolved from symbiotic bacteria. In telling the exciting story of an evolutionary biology tradition that has effectively challenged many key tenets of classical neo-Darwinism, Sapp sheds light on the phenomena, movements, doctrines, and controversies that have shaped attitudes about the scope and significance of symbiosis. Engaging and insightful, Evolution by Association will be avidly read by students and researchers across the life sciences.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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