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05 Jun 2023 at 01:46
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Bibliography on: Symbiosis


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RJR: Recommended Bibliography 05 Jun 2023 at 01:46 Created: 


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®)


RevDate: 2023-06-03

Chaisiri K, Linsuwanon P, BL Makepeace (2023)

The chigger microbiome: big questions in a tiny world.

Trends in parasitology pii:S1471-4922(23)00120-4 [Epub ahead of print].

'Chiggers' (trombiculid mite larvae) are best known as vectors of rickettsial pathogens, Orientia spp., which cause a zoonosis, scrub typhus. However, several other pathogens (e.g., Hantaan orthohantavirus, Dabie bandavirus, Anaplasma spp., Bartonella spp., Borrelia spp., and Rickettsia spp.) and bacterial symbionts (e.g., Cardinium, Rickettsiella, and Wolbachia) are being reported from chiggers with increasing frequency. Here, we explore the surprisingly diverse chigger microbiota and potential interactions within this microcosm. Key conclusions include a possible role for chiggers as vectors of viral diseases; the dominance in some chigger populations of unidentified symbionts in several bacterial families; and increasing evidence for vertical transmission of potential pathogens and symbiotic bacteria in chiggers, suggesting intimate interactions and not simply incidental acquisition of bacteria from the environment or host.

RevDate: 2023-06-03

Fardi F, Bahari Khasraghi L, Shahbakhti N, et al (2023)

An interplay between non-coding RNAs and gut microbiota in human health.

Diabetes research and clinical practice pii:S0168-8227(23)00502-8 [Epub ahead of print].

Humans have a complicated symbiotic relationship with their gut microbiome, which is postulated to impact host health and disease broadly. Epigenetic alterations allow host cells to regulate gene expression without altering the DNA sequence. The gut microbiome, offering environmental hints, can influence responses to stimuli by host cells with modifications on their epigenome and gene expression. Recent increasing data suggest that regulatory non-coding RNAs (miRNAs, circular RNAs, and long lncRNA) may affect host-microbe interactions. These RNAs have been suggested as potential host response biomarkers in microbiome-associated disorders, including diabetes and cancer. This article reviews the current understanding of the interplay between gut microbiota and non-coding RNA, including lncRNA, miRNA, and circular RNA. This can lead to a profound understanding of human disease and influence therapy. Furthermore, microbiome engineering as a mainstream strategy for improving human health has been discussed and confirms the hypothesis about a direct cross-talk between microbiome composition and non-coding RNA.

RevDate: 2023-06-03

Nakamura S, Kurata R, Tonozuka T, et al (2023)

Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.

The Journal of biological chemistry pii:S0021-9258(23)01913-0 [Epub ahead of print].

Dextran is an α-(1→6)-glucan that is synthesized by some lactic acid bacteria, and branched dextran with α-(1→2)-, α-(1→3)-, and α-(1→4)-linkages are often produced. Although many dextranases are known to act on the α-(1→6)-linkage of dextran, few studies have functionally analyzed the proteins involved in degrading branched dextran. The mechanism by which bacteria utilize branched dextran is unknown. Earlier, we identified dextranase (FjDex31A) and kojibiose hydrolase (FjGH65A) in the dextran utilization locus (FjDexUL) of a soil Bacteroidota Flavobacterium johnsoniae and hypothesized that FjDexUL is involved in the degradation of α-(1→2)-branched dextran. In this study, we demonstrate that FjDexUL proteins recognize and degrade α-(1→2)- and α-(1→3)-branched dextrans produced by Leuconostoc citreum S-32 (S-32 α-glucan). The FjDexUL gene was significantly upregulated when S-32 α-glucan was the carbon source compared with α-glucooligosaccharides and α-glucans, such as linear dextran and branched α-glucan from L. citreum S-64. FjDexUL GHs synergistically degraded S-32 α-glucan. The crystal structure of FjGH66 shows that some sugar-binding subsites can accommodate α-(1→2)- and α-(1→3)-branches. The structure of FjGH65A in complex with isomaltose supports that FjGH65A acts on α-(1→2)-glucosyl isomaltooligosaccharides. Furthermore, two cell surface sugar-binding proteins (FjDusD and FjDusE) were characterized, and FjDusD showed affinity for isomaltooligosaccharides and FjDusE for dextran, including linear and branched dextrans. Collectively, FjDexUL proteins are suggested to be involved in the degradation of α-(1→2)- and α-(1→3)-branched dextrans. Our results will be helpful in understanding the bacterial nutrient requirements and symbiotic relationships between bacteria at the molecular level.

RevDate: 2023-06-03

Pacheco R, C Quinto (2023)

Corrigendum to "Phospholipase Ds in plants: Their role in pathogenic and symbiotic interactions" [Plant Physiol. Biochem. 173 (2022) 76-86].

RevDate: 2023-06-03

Zhao Z, Wang L, Kelley K, et al (2023)

GFP labeling of a Bradyrhizobium strain and an attempt to track the crack entry process during symbiosis with peanuts.

World journal of microbiology & biotechnology, 39(8):219.

Compared to the well-studied model legumes, where symbiosis is established via root hair entry, the peanut is infected by Bradyrhizobium through the crack entry, which is less common and not fully understood. Crack entry is, however, considered a primitive symbiotic infection pathway, which could be potentially utilized for engineering non-legume species with nitrogen fixation ability. We utilized a fluorescence-labeled Bradyrhizobium strain to help in understanding the crack entry process at the cellular level. A modified plasmid pRJPaph-bjGFP, harboring the codon-optimized GFP gene and tetracycline resistance gene, was created and conjugated into Bradyrhizobium strain Lb8, an isolate from peanut nodules, through tri-parental mating. Microscopic observation and peanut inoculation assays confirmed the successful GFP tagging of Lb8, which is capable of generating root nodules. A marking system for peanut root potential infection sites and an optimized sample preparation protocol for cryostat sectioning was developed. The feasibility of using the GFP-tagged Lb8 for observing crack entry was examined. GFP signal was detected at the nodule primordial stage and the following nodule developmental stages with robust GFP signals observed in infected cells in the mature nodules. Spherical bacteroids in the root tissue were visualized at the nodules' inner cortex under higher magnification, reflecting the trace along the rhizobial infection path. The GFP labeled Lb8 can serve as an essential tool for plant-microbe studies between the cultivated peanut and Bradyrhizobium, which could facilitate further study of the crack entry process during the legume-rhizobia symbiosis.

RevDate: 2023-06-02

de Souza MR, Caruso C, Ruiz-Jones L, et al (2023)

Importance of depth and temperature variability as drivers of coral symbiont composition despite a mass bleaching event.

Scientific reports, 13(1):8957.

Coral reefs are iconic examples of climate change impacts because climate-induced heat stress causes the breakdown of the coral-algal symbiosis leading to a spectacular loss of color, termed 'coral bleaching'. To examine the fine-scale dynamics of this process, we re-sampled 600 individually marked Montipora capitata colonies from across Kāne'ohe Bay, Hawai'i and compared the algal symbiont composition before and after the 2019 bleaching event. The relative proportion of the heat-tolerant symbiont Durusdinium in corals increased in most parts of the bay following the bleaching event. Despite this widespread increase in abundance of Durusdinium, the overall algal symbiont community composition was largely unchanged, and hydrodynamically defined regions of the bay retained their distinct pre-bleaching compositions. We explain ~ 21% of the total variation, of which depth and temperature variability were the most significant environmental drivers of Symbiodiniaceae community composition by site regardless of bleaching intensity or change in relative proportion of Durusdinium. We hypothesize that the plasticity of symbiont composition in corals may be constrained to adaptively match the long-term environmental conditions surrounding the holobiont, despite an individual coral's stress and bleaching response.

RevDate: 2023-06-02

Shi G, Hou R, Li T, et al (2023)

Effects of biochar and freeze‒thaw cycles on the bacterial community and multifunctionality in a cold black soil area.

Journal of environmental management, 342:118302 pii:S0301-4797(23)01090-3 [Epub ahead of print].

Global climate change has altered soil freeze‒thaw cycle events, and little is known about soil microbe response to and multifunctionality regarding freeze‒thaw cycles. Therefore, in this study, biochar was used as a material to place under seasonal freeze-thaw cycling conditions. The purpose of this study was to explore the ability of biochar to regulate the function of freeze-thaw soil cycles to ensure spring sowing and food production. The results showed that biochar significantly increased the richness and diversity of soil bacteria before and after freezing-thawing. In the freezing period, the B50 treatment had the greatest improvement effect (2.6% and 5.5%, respectively), while in the thawing period, the B75 treatment had the best improvement effect. Biochar changed the composition and distribution characteristics of the bacterial structure and enhanced the multifunctionality of freeze-thaw soil and the stability of the bacterial symbiotic network. Compared with the CK treatment, the topological characteristics of the bacterial ecological network of the B50 treatment increased the most. They were 0.89 (Avg.degree), 9.79 (Modularity), 9 (Nodes), and 255 (Links). The freeze-thaw cycle decreased the richness and diversity of the bacterial community and changed the composition and distribution of the bacterial community, and the total bacterial population decreased by 658 (CK), 394 (B25), 644 (B50) and 86 (B75) during the thawing period compared with the freezing period. The soil multifunctionality in the freezing period was higher than that during the thawing period, indicating that the freeze-thaw cycle reduced soil ecological function. From the perspective of abiotic analysis, the decrease in soil multifunctionality was due to the decrease in soil nutrients, enzyme activities, soil basic respiration and other singular functions. From the perspective of bacteria, the decrease in soil multifunctionality was mainly due to the change in the Actinobacteriota group. This work expands the understanding of biochar ecology in cold black soil. These results are conducive to the sustainable development of soil ecological function in cold regions and ultimately ensure crop growth and food productivity.

RevDate: 2023-06-02

Yazıcı E, Alakaş HM, T Eren (2023)

Prioritizing of sectors for establishing a sustainable industrial symbiosis network with Pythagorean fuzzy AHP- Pythagorean fuzzy TOPSIS method: a case of industrial park in Ankara.

Environmental science and pollution research international [Epub ahead of print].

Difficulty in accessing resources and increasing environmental concerns encourage industrial manufacturing enterprises to establish a symbiosis network. The identification of symbiotic relationships contributes to the more sustainable development of industrial activities. However, businesses operating in industrial parks are diversified by sector. In order to establish a sustainable symbiosis network in industrial parks, the symbiotic relations of each sector in industrial parks should be evaluated separately. Thus, the installation process of the symbiosis network will be easier and more sustainable. In this context, this study aims to prioritize the sector in which a symbiosis network will be established by presenting an innovative approach for the evaluation of symbiosis potentials. For this purpose, criteria for the implementation process affecting the establishment of the symbiosis network were determined. Multi-criteria decision-making methods were used to solve the problem. Considering the uncertainties in the process, fuzzy multi-criteria decision-making methods were used. As a result, a decision-making model has been proposed to determine the priority sector in order to establish a symbiosis network in industrial parks. According to the results obtained with the multi-criteria decision-making methods, the number of enterprises that will evaluate the waste, that is, the number of customers with waste, has been determined as the criterion with the highest level of importance. While evaluating the alternatives, the casting sector was chosen as a priority. This sector is followed by the petro and chemical sector as the second alternative.

RevDate: 2023-06-02

Rodrigues J, Lefoulon E, Gavotte L, et al (2023)

Wolbachia springs eternal: symbiosis in Collembola is associated with host ecology.

Royal Society open science, 10(5):230288 pii:rsos230288.

Wolbachia are endosymbiotic alpha-proteobacteria infecting a wide range of arthropods and nematode hosts with diverse interactions, from reproductive parasites to obligate mutualists. Their taxonomy is defined by lineages called supergroups (labelled by letters of the alphabet), while their evolutionary history is complex, with multiple horizontal transfers and secondary losses. One of the least recently derived, supergroup E, infects springtails (Collembola), widely distributed hexapods, with sexual and/or parthenogenetic populations depending on species. To better characterize the diversity of Wolbachia infecting springtails, the presence of Wolbachia was screened in 58 species. Eleven (20%) species were found to be positive, with three Wolbachia genotypes identified for the first time in supergroup A. The novel genotypes infect springtails ecologically and biologically different from those infected by supergroup E. To root the Wolbachia phylogeny, rather than distant other Rickettsiales, supergroup L infecting plant-parasitic nematodes was used here. We hypothesize that the ancestor of Wolbachia was consumed by soil-dwelling nematodes, and was transferred horizontally via plants into aphids, which then infected edaphic arthropods (e.g. springtails and oribatid mites) before expanding into most clades of terrestrial arthropods and filarial nematodes.

RevDate: 2023-06-02

Smith MJ, JE Geach (2023)

Astronomia ex machina: a history, primer and outlook on neural networks in astronomy.

Royal Society open science, 10(5):221454 pii:rsos221454.

In this review, we explore the historical development and future prospects of artificial intelligence (AI) and deep learning in astronomy. We trace the evolution of connectionism in astronomy through its three waves, from the early use of multilayer perceptrons, to the rise of convolutional and recurrent neural networks, and finally to the current era of unsupervised and generative deep learning methods. With the exponential growth of astronomical data, deep learning techniques offer an unprecedented opportunity to uncover valuable insights and tackle previously intractable problems. As we enter the anticipated fourth wave of astronomical connectionism, we argue for the adoption of GPT-like foundation models fine-tuned for astronomical applications. Such models could harness the wealth of high-quality, multimodal astronomical data to serve state-of-the-art downstream tasks. To keep pace with advancements driven by Big Tech, we propose a collaborative, open-source approach within the astronomy community to develop and maintain these foundation models, fostering a symbiotic relationship between AI and astronomy that capitalizes on the unique strengths of both fields.

RevDate: 2023-06-02

Gu Y, Han W, Wang Y, et al (2023)

Xylocopa caerulea and Xylocopa auripennis harbor a homologous gut microbiome related to that of eusocial bees.

Frontiers in microbiology, 14:1124964.

BACKGROUND: Eusocial bees, such as bumblebees and honey bees, harbor host-specific gut microbiota through their social behaviors. Conversely, the gut microbiota of solitary bees is erratic owing to their lack of eusocial activities. Carpenter bees (genus Xylocopa) are long-lived bees that do not exhibit advanced eusociality like honey bees. However, they often compete for nests to reproduce. Xylocopa caerulea and Xylocopa auripennis are important pollinators of wild plants on Hainan Island. Whether they have host-specific bacteria in their guts similar to eusocial bees remains unknown.

METHODS: We targeted the bacterial 16S rRNA V3-V4 region to investigate the diversity of bacterial symbionts in the fore-midgut and hindgut of two carpenter bees, X. caerulea and X. auripennis.

RESULTS: A maximum of 4,429 unique amplicon sequence variants (ASVs) were detected from all samples, belonging to 10 different phyla. X. caerulea and X. auripennis shared similar bacterial community profiles, with Lactobacillaceae, Bifidobacteriaceae, and Orbaceae being dominant in their entire guts. X. caerulea and X. auripennis harbor a highly conserved core set of bacteria, including the genera Candidatus Schmidhempelia and Bombiscardovia. These two bacterial taxa from carpenter bees are closely related to those isolated from bumblebees. The LEfSe analysis showed that Lactobacillaceae, Bifidobacteriaceae, and the genus Bombilactobacillus were significantly enriched in the hindguts of both carpenter bees. Functional prediction suggested that the most enriched pathways were involved in carbohydrate and lipid metabolism.

CONCLUSIONS: Our results revealed the structure of the gut microbiota in two carpenter bees and confirmed the presence of some core bacterial taxa that were previously only found in the guts of social bees.

RevDate: 2023-06-02

N M Furtado A, Leonardi M, Comandini O, et al (2023)

Restinga ectomycorrhizae: a work in progress.

F1000Research, 12:317.

Background: The Brazilian Atlantic Forest is one of the most biodiverse terrestrial ecoregions of the world. Among its constituents, restinga vegetation makes a particular case, acting as a buffer zone between the oceans and the forest. Covering some 80% of Brazilian coastline (over 7,300 km in length), restinga is a harsh environment where plants and fungi interact in complex ways that just now are beginning to be unveiled. Ectomycorrhizal symbiosis, in particular, plays a so far ungauged and likely underestimated role. We recently described the morpho-anatomical and molecular features of the ectomycorrhizae formed by several basidiomycetous mycobionts on the host plant Guapira opposita, but the mycorrhizal biology of restinga is still largely unexplored. Here, we report new data on the ectomycorrhizal fungal symbionts of G. opposita, based on the collection of sporomata and ectomycorrhizal root tips in restinga stands occurring in southern Brazil. Methods: To obtain a broader view of restinga mycorrhizal and ecological potential, we compiled a comprehensive and up-to-date checklist of fungal species reported or supposed to establish ectomycorrhizae on restinga-inhabiting host plants, mainly on the basis of field observations. Results: Our list comprises some 726 records, 74 of which correspond to putative ectomycorrhizal taxa specifically associated with restinga. These include several members of Boletaceae, Amanita, Tomentella/ Thelephora, Russula/ Lactifluus, and Clavulina, as well as hypogeous fungi, like the recently described Longistriata flava. Conclusions: Our survey reveals a significant diversity of the restinga ectomycorrhizal mycobiota, indicating the importance of this symbiosis for the ecological functioning of a unique yet poorly known and threatened ecosystem.

RevDate: 2023-06-02

Windsor FM (2023)

Expanding network ecology in freshwater ecosystems.

The Journal of animal ecology [Epub ahead of print].

Research in freshwater ecosystems has always had a strong focus on ecological interactions. The vast majority of studies, however, have investigated trophic interactions and food webs, overlooking a wider suite of non-trophic interactions (e.g. facilitation, competition, symbiosis and parasitism) and the ecological networks they form. Without a complete understanding of all potential interactions, ranging from mutualistic through to antagonistic, we may be missing important ecological processes with consequences for ecosystem assembly, structure and function. Ecological networks can be constructed at different scales, from genes to ecosystems, but also local to global, and as such there is significant opportunity to put them to work in freshwater research. To expand beyond food webs, we need to leverage technological and methodological advances and look to recent research in marine and terrestrial systems-which are far more advanced in terms of detecting, measuring and contextualising ecological interactions. Future studies should look to emerging technologies to aid in merging the wide range of ecological interactions in freshwater ecosystems into networks to advance our understanding and ultimately increase the efficacy of conservation, management, restoration and other applications.

RevDate: 2023-06-01

Wicaksono WA, Semler B, Pöltl M, et al (2023)

The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts.

Environmental microbiome, 18(1):46.

BACKGROUND: The microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated with Riccia temporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria and Burgenland, Austria combining qPCR analyses, amplicon sequencing and advanced microscopy.

RESULTS: Riccia spec. div. was colonized by a very high abundance of bacteria (10[10] 16S rRNA gene copies per g of thallus) as well as archaea and fungi (10[8] ITS copies per g of thallus). Each Riccia thallus contain approx. 1000 prokaryotic and fungal ASVs. The field type was the main driver for the enrichment of fungal taxa, likely due to an imprint on soil microbiomes by the cultivated crop plants. This was shown by a higher fungal richness and different fungal community compositions comparing liverwort samples collected from pumpkin fields, with those from corn fields. In contrast, bacterial communities linked to liverworts are highly specialized and the soil attached to them is not a significant source of these bacteria. Specifically, enriched Cyanobacteria, Bacteroidetes and Methylobacteria suggest a symbiotic interaction. Intriguingly, compared to the surrounding soil, the thallus samples were shown to enrich several well-known bacterial and fungal phytopathogens indicating an undescribed role of liverworts as potential reservoirs of crop pathogens.

CONCLUSIONS: Our results provide evidence that a stable bacterial community but varying fungal communities are colonizing liverwort thalli. Post-harvest, temporary agricultural biocrusts are important reservoirs for microbial biodiversity but they have to be considered as potential reservoirs for pathogens as well.

RevDate: 2023-06-01

Sen A, Tanguy G, Galand PE, et al (2023)

Bacterial symbiont diversity in Arctic seep Oligobrachia siboglinids.

Animal microbiome, 5(1):30.

BACKGROUND: High latitude seeps are dominated by Oligobrachia siboglinid worms. Since these worms are often the sole chemosymbiotrophic taxon present (they host chemosynthetic bacteria within the trophosome organ in their trunk region), a key question in the study of high latitude seep ecology has been whether they harbor methanotrophic symbionts. This debate has manifested due to the mismatch between stable carbon isotope signatures of the worms (lower than -50‰ and usually indicative of methanotrophic symbioses) and the lack of molecular or microscopic evidence for methanotrophic symbionts. Two hypotheses have circulated to explain this paradox: (1) the uptake of sediment carbon compounds with depleted δC[13] values from the seep environment, and (2) a small, but significant and difficult to detect population of methanotrophic symbionts. We conducted 16S rRNA amplicon sequencing of the V3-V4 regions on two species of northern seep Oligobrachia (Oligobrachia webbi and Oligobrachia sp. CPL-clade), from four different high latitude sites, to investigate the latter hypothesis. We also visually checked the worms' symbiotic bacteria within the symbiont-hosting organ, the trophosome, through transmission electron microscopy.

RESULTS: The vast majority of the obtained reads corresponded to sulfide-oxidizers and only a very small proportion of the reads pertained to methane-oxidizers, which suggests a lack of methanotrophic symbionts. A number of sulfur oxidizing bacterial strains were recovered from the different worms, however, host individuals tended to possess a single strain, or sometimes two closely-related strains. However, strains did not correspond specifically with either of the two Oligobrachia species we investigated. Water depth could play a role in determining local sediment bacterial communities that were opportunistically taken up by the worms. Bacteria were abundant in non-trophosome (and thereby symbiont-free) tissue and are likely epibiotic or tube bacterial communities.

CONCLUSIONS: The absence of methanotrophic bacterial sequences in the trophosome of Arctic and north Atlantic seep Oligobrachia likely indicates a lack of methanotrophic symbionts in these worms, which suggests that nutrition is sulfur-based. This is turn implies that sediment carbon uptake is responsible for the low δ[13]C values of these animals. Furthermore, endosymbiotic partners could be locally determined, and possibly only represent a fraction of all bacterial sequences obtained from tissues of these (and other) species of frenulates.

RevDate: 2023-06-01

Noel B, Denoeud F, Rouan A, et al (2023)

Pervasive tandem duplications and convergent evolution shape coral genomes.

Genome biology, 24(1):123.

BACKGROUND: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species.

RESULTS: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience.

CONCLUSIONS: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

RevDate: 2023-06-01

Veglia AJ, Bistolas KSI, Voolstra CR, et al (2023)

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.

Communications biology, 6(1):566.

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

RevDate: 2023-06-01

Belser C, Poulain J, Labadie K, et al (2023)

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.

Scientific data, 10(1):326.

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

RevDate: 2023-06-01

Yee DP, Samo TJ, Abbriano RM, et al (2023)

The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis.

Current biology : CB pii:S0960-9822(23)00615-2 [Epub ahead of print].

Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.[1] These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.[2] However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H[+]-ATPase (VHA),[3] proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.[4][,][5] We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates[6][,][7][,][8] provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.

RevDate: 2023-06-01

Hong H, Wang L, Y Qi (2023)

Characteristics of the oropharyngeal microbiota among infants with pneumonia and their effects on immune response and subsequent respiratory morbidity.

European journal of pediatrics [Epub ahead of print].

UNLABELLED: Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown. The present study aimed to analyze the oropharyngeal microbiota of infants with pneumonia and to explore the impact of disturbances of the microbiota on disease severity and long-term respiratory morbidities. The oropharyngeal microbiome was characterized using 16S ribosomal RNA-based sequencing, while serum immune mediators were assessed using cytometric bead array, and invariant natural killer T (iNKT) cells were detected using flow cytometry in infants with pneumonia < 6 months of age. Patients were followed up to 3 years of age, and clinical and respiratory morbidity data were collected. A total of 106 infants with pneumonia were enrolled in this study. Diversity of the respiratory microbiota was inversely correlated with the severity of pneumonia and length of hospitalization. Patients who experienced wheezing during pneumonia exhibited lower percentages of total iNKT cells, CD8-positive (+), and CD4-CD8- subsets, and higher CD4 + subsets than those without. The relative abundances of Prevotella and Veillonella species were lower in patients with severe pneumonia. The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing than in those without wheezing. The relative abundance and total counts of Bifidobacterium, Lactobacillus, and Neisseria were higher in patients who did not experience subsequent recurrent wheezing.

CONCLUSIONS: Diversity of the respiratory microbiota was inversely associated with pneumonia severity, and the percentage of iNKT cells was associated with wheezing during pneumonia. Several species may be associated with subsequent respiratory morbidities and warrant further investigation.

WHAT IS KNOWN: • Early life airway microbiota symbiosis affects the severity of respiratory infection and the risk for the development of asthma. • Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown.

WHAT IS NEW: • The diversity of the airway microbiome was inversely associated with the severity of pneumonia and length of hospitalization. • The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing.

RevDate: 2023-06-01

Lu Y, Lin Y, Li M, et al (2023)

Roles of Streptococcus mutans-Candida albicans interaction in early childhood caries: a literature review.

Frontiers in cellular and infection microbiology, 13:1151532.

As one of the most common oral diseases in kids, early childhood caries affects the health of children throughout the world. Clinical investigations show the copresence of Candida albicans and Streptococcus mutans in ECC lesions, and mechanistic studies reveal co-existence of C. albicans and S. mutans affects both of their cariogenicity. Clearly a comprehensive understanding of the interkingdom interaction between these two microorganisms has important implications for ECC treatment and prevention. To this end, this review summarizes advances in our understanding of the virulence of both C. albicans and S. mutans. More importantly, the synergistic and antagonistic interactions between these two microbes are discussed.

RevDate: 2023-06-01

Ballesteros-Gutiérrez M, Albareda M, Barbas C, et al (2023)

A host-specific diaminobutyrate aminotransferase contributes to symbiotic performance, homoserine metabolism, and competitiveness in the Rhizobium leguminosarum/Pisum sativum system.

Frontiers in microbiology, 14:1182563.

Rhizobium leguminosarum bv. viciae (Rlv) UPM791 effectively nodulates pea and lentil, but bacteroids contain a number of proteins differentially expressed depending on the host. One of these host-dependent proteins (C189) is similar to a diaminobutyrate-2-oxoglutarate aminotransferase (DABA-AT). DABA-AT activity was demonstrated with cell extracts and with purified protein, so C189 was renamed as Dat. The dat gene was strongly induced in the central, active area of pea nodules, but not in lentil. Mutants defective in dat were impaired in symbiotic performance with pea plants, exhibiting reduced shoot dry weight, smaller nodules, and a lower competitiveness for nodulation. In contrast, there were no significant differences between mutant and wild-type in symbiosis with lentil plants. A comparative metabolomic approach using cell-free extracts from bacteroids induced in pea and lentil showed significant differences among the strains in pea bacteroids whereas no significant differences were found in lentil. Targeted metabolomic analysis revealed that the dat mutation abolished the presence of 2,4-diaminobutyrate (DABA) in pea nodules, indicating that DABA-AT reaction is oriented toward the production of DABA from L-aspartate semialdehyde. This analysis also showed the presence of L-homoserine, a likely source of aspartate semialdehyde, in pea bacteroids but not in those induced in lentil. The dat mutant showed impaired growth when cells were grown with L-homoserine as nitrogen source. Inclusion of DABA or L-homoserine as N source suppressed pantothenate auxotropy in Rlv UPM791, suggesting DABA as source of the pantothenate precursor β-alanine. These data indicate that Rlv UPM791 Dat enzyme is part of an adaptation mechanism of this bacterium to a homoserine-rich environment such as pea nodule and rhizosphere.

RevDate: 2023-05-31

Garritano AN, Majzoub ME, Ribeiro B, et al (2023)

Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae.

The ISME journal [Epub ahead of print].

Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp., Farrea sp. and Paratimea sp.. Given the known autotrophic metabolism of AOAs, this implies that these sponge holobionts can have the capacity for primary production in the deep-sea. We also show that specific AOA lineages are highly specific towards their hosts, hinting towards an unprecedent vertical transmission of these symbionts in deep-sea sponges. Our results show that the ecology and evolution of symbiotic relationships in deep-sea sponge is distinct from that of their shallow-water counterparts.

RevDate: 2023-05-31

Teulet A, Quan C, Evangelisti E, et al (2023)

A pathogen effector FOLD diversified in symbiotic fungi.

The New phytologist [Epub ahead of print].

Pathogenic fungi use secreted effector proteins to suppress immunity and support their infection, but effectors have also been reported from fungi that engage in nutritional symbioses with plants. Sequence-based effector comparisons between pathogens and symbiotic arbuscular mycorrhizal (AM) fungi are hampered by the huge diversity of effector sequences even within closely related microbes. To find sequence-divergent but structurally similar effectors shared between symbiotic and pathogenic fungi, we compared secreted protein structure models of the AM fungus Rhizophagus irregularis to known pathogen effectors. We identified proteins with structural similarity to known Fusarium oxysporum f. sp. lycopersici dual domain (FOLD) effectors, which occur in low numbers in several fungal pathogens. Contrastingly, FOLD genes from AM fungi (MycFOLDs) are found in enlarged and diversified gene families with higher levels of positive selection in their C-terminal domains. Our structure model comparison suggests that MycFOLDs are similar to carbohydrate-binding motifs. Different MycFOLD genes are expressed during colonisation of different hosts and MycFOLD-17 transcripts accumulate in plant intracellular arbuscules. The exclusive presence of MycFOLDs across unrelated plant-colonising fungi, their inducible expression, lineage-specific sequence diversification and transcripts in arbuscules suggest that FOLD proteins act as effectors during plant colonisation of symbiotic and pathogenic fungi.

RevDate: 2023-05-31

Costa-Conceicao K, Villamar Ayala CA, Dávila T, et al (2023)

Performance of hybrid biofilter based on rice husks/sawdust treating grey wastewater.

Water science and technology : a journal of the International Association on Water Pollution Research, 87(10):2416-2431.

An innovative nature-based technology for wastewater treatment is the hybrid biofiltration, which combines complex symbiotic relationships between plants, earthworms and microorganisms with adequate support components. This latter could be optimized using organic supports. The aim of this research was to evaluate the performance of hybrid biofilters based on rice husks/sawdust treating grey wastewater from mining camps. Four biofilters using an active layer (rice husks/sawdust: 50/50%, v/v) at 60(B60) and 45(B45) cm height and operating for 64 days at a hydraulic loading rate between 1 and 5 m[3]/m[2]d were monitored. Eisenia foetida Savigny and Cyperus papyrus L. were used as a biotic component. COD, N-NH4[+], NO3[-], NO2[-], PO4[3-] and fecal coliforms were weekly monitored. Results showed that the most efficient HB was using 60 cm as an active layer and operating at 3 m[3]/m[2]d, which reported average removal efficiencies for COD, NH4[+], NO3[-], PO4[3-] and fecal coliforms up to 85, 89, 47, 49 and 99.9%, respectively. Organic support improved the rate growth for Cyperus papirus L. and E. foetida Savigny up to 50%. Hybrid biofiltration using organic residues is low-cost, providing all-encompassing operational and performance features, improving the wastewater reclamation opportunities.

RevDate: 2023-05-31

Mihirogi Y, Kaneda M, Yamagishi D, et al (2023)

Establishment of a New Model Sea Anemone for Comparative Studies on Cnidarian-Algal Symbiosis.

Zoological science, 40(3):235-245.

Frequent coral bleaching has drawn attention to the mechanisms of coral dinoflagellate endosymbiosis. Owing to the difficulty of rearing corals in the laboratory, model symbiosis systems are desired. The sea anemone Exaiptasia diaphana, hosting clade B1 of the genus Breviolum, has long been studied as a model system; however, a single species is insufficient for comparative studies and thus provides only limited resources for symbiosis research, especially regarding the specificity of host-symbiont associations. We established a clonal strain of the sea anemone Anthopleura atodai, whose symbiont was identified as a novel subclade of Symbiodinium (clade A) using a novel feeding method. We also developed a method to efficiently bleach various sea anemone species using a quinoclamine-based herbicide. Bleached A. atodai polyps were vital and able to reproduce asexually, exhibiting no signs of harmful effects of the drug treatment. Pilot studies have suggested that host-symbiont specificity is influenced by multiple steps differently in A. atodai and E. diaphana. RNAseq analyses of A. atodai showed that multiple NPC2 genes were expressed in the symbiotic state, which have been suggested to function in the transport of sterols from symbionts to host cells. These results reveal the usefulness of A. atodai in comparative studies of cnidarian-algal symbiosis.

RevDate: 2023-05-31

Kobayashi G, Itoh H, N Nakajima (2023)

Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes.

Zoological science, 40(3):224-234.

Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.

RevDate: 2023-05-31

Kaur S, Espinosa-Sáiz D, Velázquez E, et al (2023)

Complete Genome Sequences of the Species Type Strains Sinorhizobium garamanticum LMG 24692 and Sinorhizobium numidicum LMG 27395 and CIP 109850.

Microbiology resource announcements [Epub ahead of print].

The genus Sinorhizobium comprises rhizobia that fix nitrogen in symbiosis with legumes. To support taxonomic studies of this genus and of rhizobia more broadly, we report complete genome sequences and annotations for the species type strains Sinorhizobium garamanticum LMG 24692 and Sinorhizobium numidicum LMG 27395 and CIP 109850.

RevDate: 2023-05-31

Wangthaisong P, Piromyou P, Songwattana P, et al (2023)

The Type IV Secretion System (T4SS) Mediates Symbiosis between Bradyrhizobium sp. SUTN9-2 and Legumes.

Applied and environmental microbiology [Epub ahead of print].

There has been little study of the type IV secretion system (T4SS) of bradyrhizobia and its role in legume symbiosis. Therefore, broad host range Bradyrhizobium sp. SUTN9-2 was selected for study. The chromosome of Bradyrhizobium sp. SUTN9-2 contains two copies of the T4SS gene, homologous with the tra/trb operons. A phylogenetic tree of the T4SS gene traG was constructed, which exemplified its horizontal transfer among Bradyrhizobium and Mesorhizobium genera. They also showed similar gene arrangements for the tra/trb operons. However, the virD2 gene was not observed in Mesorhizobium, except M. oppotunistum WSM2075. Interestingly, the orientation of copG, traG, and virD2 cluster was unique to the Bradyrhizobium genus. The phylogenetic tree of copG, traG, and virD2 demonstrated that copies 1 and 2 of these genes were grouped in different clades. In addition, the derived mutant and complementation strains of T4SS were investigated in representative legumes Genistoids, Dalbergioids, and Millettiods. When T4SS copy 1 (T4SS1) was deleted, the nodule number and nitrogenase activity decreased. This supports a positive effect of T4SS1 on symbiosis. In addition, delayed nodulation was observed 7 dpi, which was restored by the complementation of T4SS1. Therefore, T4SS plays an important role in the symbiotic interaction between Bradyrhizobium sp. SUTN9-2 and its leguminous hosts. IMPORTANCE SUTN9-2 is a broad host range strain capable of symbiosis with several legumes. Two copies of T4SS clusters belonging to the tra/trb operon are observed on chromosomes with different gene arrangements. We use phylogenetic tree and gene annotation analysis to predict the evolution of the tra/trb operon of rhizobia. Our finding suggests that the gene encoding the T4SS gene among Bradyrhizobium and Mesorhizobium may have coevolution. In addition, Bradyrhizobium has a uniquely arranged copG, traG, and virD2 gene cluster. The results of T4SS1 gene deletion and complementation revealed its positive effect on nodulation. Therefore, T4SS seems to be another determinant for symbiosis. This is the first report on the role of T4SS in Bradyrhizobium symbiosis.

RevDate: 2023-05-31

Rich M (2023)

Phylogenomics reveal that plants colonized land together with their fungal symbiotic partners.

Comptes rendus biologies, 346:1-11.

Most extant land plants establish a mutually beneficial relationship with soil fungi called mycorrhizal symbiosis. From their partners, plants get access to mineral nutrient and water resources transported via a fungal network that acts like an extension of their root systems. Using genetic and molecular tools, we showed that distant plant species use similar molecular mechanisms during the symbiosis. This similarity suggests that those mechanisms were inherited from their last common ancestor, a lineage that emerged from an aquatic environment 450 million years ago. Thus, this plant fungal interaction could have helped the first land plants without structures adapted to soil exploration to survive and colonize this new environment.

RevDate: 2023-05-31

López-García P, D Moreira (2023)

The symbiotic origin of the eukaryotic cell.

Comptes rendus biologies, 346:55-73.

Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.

RevDate: 2023-05-30

Kim JY, Yi MH, Kim M, et al (2023)

Production of Dermatophagoides farinae Having Low Bacterial Content Using Ampicillin.

Journal of immunology research, 2023:9024595.

BACKGROUND: Symbiotic bacteria in house dust mites pose a risk of immunological side effects in the clinical use of immunotherapeutic agents. In this study, we investigated the duration for which the bacterial concentration in Dermatophagoides farinae could be kept low with antibiotic treatment, and whether the allergenic properties of the mite changed under ampicillin treatment.

METHODS: D. farinae was cultivated in the presence of ampicillin powder in an autoclaved medium for 6 weeks. After subsequent subcultures without ampicillin, the mites were harvested, and the extract was prepared. The amounts of bacteria, lipopolysaccharides (LPS), and two major allergens (Der f 1 and Der f 2) were measured. Human bronchial epithelial cells and mice were treated with the D. farinae extract to assess the allergic airway inflammation.

RESULTS: The number of bacteria and level of LPS were reduced by 150-fold and 33-fold, respectively, at least 18 weeks after ampicillin treatment. The concentration of Der f 1 and Der f 2 remained unchanged by ampicillin treatment. The secretion of interleukin (IL)-6 and IL-8 from the human airway epithelial cells decreased when treated with the extract of ampicillin-treated D. farinae compared with that of ampicillin-untreated D. farinae. A mouse asthma model was developed using ampicillin-treated D. farinae. We observed that the level of lung function, airway inflammation, and serum-specific immunoglobulin were not different for the mouse asthma model developed using ampicillin-treated D. farinae than the model developed using ampicillin-untreated D. farinae.

CONCLUSIONS: We showed that bacterial content in D. farinae was reduced by ampicillin treatment, which was sufficient to induce allergic sensitization and an immune response. This method will be used to develop more controlled allergy immunotherapeutic agents.

RevDate: 2023-05-30

Cossart P, Kolter R, Lemaitre B, et al (2023)

The New Microbiology: an international lecture course on the island of Spetses.

microLife, 4:uqac026.

In September 2022, an international summer course entitled 'The new microbiology' took place in Greece, on the island of Spetses. The organizers aimed to highlight the spectacular advances and the renaissance occurring in Microbiology, driven by developments in genomics, proteomics, imaging techniques, and bioinformatics. Combinations of these advances allow for single cell analyses, rapid and relatively inexpensive metagenomic and transcriptomic data analyses and comparisons, visualization of previously unsuspected mechanisms, and large-scale studies. A 'New Microbiology' is emerging which allows studies that address the critical roles of microbes in health and disease, in humans, animals, and the environment. The concept of one health is now transforming microbiology. The goal of the course was to discuss all these topics with members of the new generation of microbiologists all of whom were highly motivated and fully receptive.

RevDate: 2023-05-30

Wu-Chuang A, Hartmann D, Maitre A, et al (2023)

Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae.

Microbial ecology [Epub ahead of print].

Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.

RevDate: 2023-05-30

Fields B, Moeskjaer S, Deakin WJ, et al (2023)

Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions.

Molecular ecology [Epub ahead of print].

While shaping of plant microbiome composition through 'host filtering' is well documented in legume-rhizobium symbioses, it is less clear to what extent different varieties and genotypes of the same plant species differentially influence symbiont community diversity and composition. Here, we compared how clover host varieties and genotypes affect the structure of Rhizobium populations in root nodules under conventional field and controlled greenhouse conditions. We first grew four Trifolium repens (white clover) F2 crosses and one variety in a conventional field trial and compared differences in root nodule Rhizobium leguminosarum symbiovar trifolii (Rlt) genotype diversity using high-throughput amplicon sequencing of chromosomal housekeeping (rpoB and recA) genes and auxiliary plasmid-borne symbiosis genes (nodA and nodD). We found that Rlt nodule diversities significantly differed between clover crosses, potentially due to host filtering. However, variance in Rlt diversity largely overlapped between crosses and was also explained by the spatial distribution of plants in the field, indicative of the role of local environmental conditions for nodule diversity. To test the effect of host filtering, we conducted a controlled greenhouse trial with a diverse Rlt inoculum and several host genotypes. We found that different clover varieties and genotypes of the same variety selected for significantly different Rlt nodule communities and that the strength of host filtering (deviation from the initial Rhizobium inoculant composition) was positively correlated with the efficiency of symbiosis (rate of plant greenness colouration). Together, our results suggest that selection by host genotype and local growth conditions jointly influence white clover Rlt nodule diversity and community composition.

RevDate: 2023-05-29

Liu Y, Shu X, Chen L, et al (2023)

Plant commensal type VII secretion system causes iron leakage from roots to promote colonization.

Nature microbiology [Epub ahead of print].

Competition for iron is an important factor for microbial niche establishment in the rhizosphere. Pathogenic and beneficial symbiotic bacteria use various secretion systems to interact with their hosts and acquire limited resources from the environment. Bacillus spp. are important plant commensals that encode a type VII secretion system (T7SS). However, the function of this secretion system in rhizobacteria-plant interactions is unclear. Here we use the beneficial rhizobacterium Bacillus velezensis SQR9 to show that the T7SS and the major secreted protein YukE are critical for root colonization. In planta experiments and liposome-based experiments demonstrate that secreted YukE inserts into the plant plasma membrane and causes root iron leakage in the early stage of inoculation. The increased availability of iron promotes root colonization by SQR9. Overall, our work reveals a previously undescribed role of the T7SS in a beneficial rhizobacterium to promote colonization and thus plant-microbe interactions.

RevDate: 2023-05-29

Peters EE, Cahn JKB, Lotti A, et al (2023)

Distribution and diversity of 'Tectomicrobia', a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites.

ISME communications, 3(1):50.

Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus 'Entotheonella' has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested 'Entotheonella' as the first members of a new candidate phylum, 'Tectomicrobia'. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that 'Entotheonella' and other 'Tectomicrobia' are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described 'Entotheonella' lineage can be more accurately divided into at least three different candidate genera with the terrestrial 'Candidatus Prasianella', the largely terrestrial 'Candidatus Allonella', the 'Candidatus Thalassonella' comprising sponge-associated members, and the more widely distributed 'Candidatus Entotheonella'. Genomic characterization of 'Thalassonella' members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to 'Entotheonella' regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised 'Entotheonella' 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich 'Entotheonella' variants, and led to the identification of the first 'Entotheonella' symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of 'Entotheonella'-based chemical symbiosis.

RevDate: 2023-05-29

Shi J, Wang W, Wang F, et al (2023)

Efficient inactivation of harmful algae K. mikimotoi by a novel algicidal bacterium via a rare direct contact pathway: Performances and mechanisms.

The Science of the total environment pii:S0048-9697(23)03022-X [Epub ahead of print].

Harmful algal blooms (HABs) caused by Karenia mikimotoi have posed great threats to marine ecosystems, and algal inactivation by symbiotic bacteria has been recognized as environmental benign methods for controlling HABs. However, the identified algicidal bacteria for K. mikimotoi is limited and exclusively based on indirect algicidal pathways, which may cause secondary pollution due to releasing toxic algicidal agents. In this study, a novel strain of algicidal bacteria Tenacibaculum sp. GD3 was isolated from the phycosphere of K. mikimotoi. The bacterial strain GD3 could achieve 92.6 % of inactivation efficiency against K. mikimotoi within 8 h of co-culturing period, which outperformed those in existing literatures reported so far. The algicidal mechanisms were revealed to be a rare direct cell-to-cell contact pathway, and the GD3 could grow by utilizing metabolites from K. mikimotoi, exhibiting excellent bacterial adaptability in the phycosphere. Cell morphology changes were monitored by live cell imaging system combined with SEM and TEM observations, which showed that the GD3 was first attached to the algal cell membrane, followed by lipid peroxidation and lysis of membrane protein. Oxidative stress responses were induced as reveled by up-regulation of intracellular ROSs and antioxidant enzyme activity. Photosynthetic parameters including rETRmax, Fv/Fm, YII and NPQ were reduced, and expression of functional genes involved in decomposition of chlorophyll and cell wall was significantly suppressed. Moreover, the intracellular release profile and acute toxicity assessment indicated that the GD3 could also detoxify the K. mikimotoi cultures and the released biomolecules would not cause adverse effect to marine environment. This study not only provides a novel algicidal bacterium against K. mikimotoi via a rare direct mode, but also helps to better understand the algicidal mechanisms at physiological and genetic level, thus moving forward the areas of HABs control by microbiological strategies.

RevDate: 2023-05-28

Gong X, Ge Z, Ma Z, et al (2023)

Effect of different size microplastic particles on the construction of algal-bacterial biofilms and microbial communities.

Journal of environmental management, 343:118246 pii:S0301-4797(23)01034-4 [Epub ahead of print].

Algal-bacterial symbiotic system is a biological purification system that combines sewage treatment with resource utilization and has the dual effects of carbon sequestration and pollution reduction. In this study, an immobilized algal-bacterial biofilm system was constructed for the treatment of natural sewage. Effects of exposure to microplastics (MPs) with different particle diameters (0.065 μm, 0.5 μm and 5 μm) were determined in terms of algal biomass recovery efficiency, the composition of extracellular polymeric substances (EPS) and morphologic characteristics. The impacts of MPs on the bacterial diversity and community structure of biofilms were also examined. The metagenomic analysis of key microorganisms and related metabolism pathways involved in system was further investigated. Results showed that following exposure to 5 μm MP, a maximum algal recovery efficiency of 80% was achieved, with a minimum PSII primary light energy conversion efficiency (Fv/Fm ratio) of 0.513. Furthermore, 5 μm MP caused the highest level of damage to the algal-bacterial biofilm, enhancing the secretion of protein-rich EPS. The biofilm morphology became rough and loose following exposure to 0.5 μm and 5 μm MP. Community diversity and richness were significantly high in biofilms exposed to 5 μm MP. Proteobacteria (15.3-24.1%), Firmicutes (5.0-7.8%) and Actinobacteria (4.2-4.9%) were dominant in all groups, with exposure to 5 μm MP resulting in the highest relative abundance for these species. The addition of MPs promoted the related metabolic functions while inhibited the degradation of harmful substances by algal-bacterial biofilms. The findings have environmental significance for the practical application of algal-bacterial biofilms for sewage treatment, providing novel insights into the potential effects of MPs on immobilized algal-bacterial biofilm systems.

RevDate: 2023-05-27

Abdi N, Van Biljon A, Steyn C, et al (2023)

Zn Fertilizer and Mycorrhizal Inoculation Effect on Bread Wheat Cultivar Grown under Water Deficit.

Life (Basel, Switzerland), 13(5): pii:life13051078.

During drought stress, many enzymes are inactivated in plants due to Zn deficiency. Zn application and arbuscular mycorrhiza fungi (AMF)-wheat symbiosis reportedly improve the tolerance of plants to drought stress. This study was done to investigate the effect of Zn and AMF on plant growth, yield attributes, relative water content (RWC), harvest index (HI), photosynthetic activity, solute accumulation, glycine betaine (GB) accumulation, antioxidant activities [(catalase (CAT) and superoxide dismutase (SOD)], and ionic attributes in a bread wheat cultivar (SST806) under drought-stress in plants grown under greenhouse conditions. Zn application and AMF inoculation, separately and combined, enhanced all plant growth parameters and yield. Root dry weight (RDW) was increased by 25, 30, and 46% for these three treatments, respectively, under drought conditions compared to the control treatment. Overall, Zn application, AMF inoculation, and their combination increased protein content, RWC, and harvest index (HI) under drought stress. However, AMF inoculation improved proline content more than Zn application under the same conditions. Regarding GB accumulation, AMF, Zn, and the combination of Zn and AMF increased GB under drought compared to well-watered conditions by 31.71, 10.36, and 70.70%, respectively. For the antioxidant defense, AMF inoculation and Zn application improved SOD and CAT activity by 58 and 56%, respectively. This study showed that Zn and/or AMF increased antioxidant levels and ionic attributes under abiotic stress.

RevDate: 2023-05-27

Zuccaro V, Ponziani FR, R Bruno (2023)

Editorial of Special Issues "Gut Microbiota-Host Interactions: From Symbiosis to Dysbiosis 2.0".

International journal of molecular sciences, 24(10): pii:ijms24108977.

The gastrointestinal (GI) tract is where external agents meet the internal environment [...].

RevDate: 2023-05-27

Jia Y, Y Li (2023)

Genome-Wide Identification and Comparative Analysis of RALF Gene Family in Legume and Non-Legume Species.

International journal of molecular sciences, 24(10): pii:ijms24108842.

Rapid alkalinization factor (RALF) are small secreted peptide hormones that can induce rapid alkalinization in a medium. They act as signaling molecules in plants, playing a critical role in plant development and growth, especially in plant immunity. Although the function of RALF peptides has been comprehensively analyzed, the evolutionary mechanism of RALFs in symbiosis has not been studied. In this study, 41, 24, 17 and 12 RALFs were identified in Arabidopsis, soybean, Lotus and Medicago, respectively. A comparative analysis including the molecular characteristics and conserved motifs suggested that the RALF pre-peptides in soybean represented a higher value of isoelectric point and more conservative motifs/residues composition than other species. All 94 RALFs were divided into two clades according to the phylogenetic analysis. Chromosome distribution and synteny analysis suggested that the expansion of the RALF gene family in Arabidopsis mainly depended on tandem duplication, while segment duplication played a dominant role in legume species. The expression levels of most RALFs in soybean were significantly affected by the treatment of rhizobia. Seven GmRALFs are potentially involved in the release of rhizobia in the cortex cells. Overall, our research provides novel insights into the understanding of the role of the RALF gene family in nodule symbiosis.

RevDate: 2023-05-27

Mohammad Aslam S, Vass I, M Szabó (2023)

Characterization of the Flash-Induced Fluorescence Wave Phenomenon in the Coral Endosymbiont Algae, Symbiodiniaceae.

International journal of molecular sciences, 24(10): pii:ijms24108712.

The dinoflagellate algae, Symbiodiniaceae, are significant symbiotic partners of corals due to their photosynthetic capacity. The photosynthetic processes of the microalgae consist of linear electron transport, which provides the energetic balance of ATP and NADPH production for CO2 fixation, and alternative electron transport pathways, including cyclic electron flow, which ensures the elevated ATP requirements under stress conditions. Flash-induced chlorophyll fluorescence relaxation is a non-invasive tool to assess the various electron transport pathways. A special case of fluorescence relaxation, the so-called wave phenomenon, was found to be associated with the activity of NAD(P)H dehydrogenase (NDH) in microalgae. We showed previously that the wave phenomenon existed in Symbiodiniaceae under acute heat stress and microaerobic conditions, however, the electron transport processes related to the wave phenomenon remained unknown. In this work, using various inhibitors, we show that (i) the linear electron transport has a crucial role in the formation of the wave, (ii) the inhibition of the donor side of Photosystem II did not induce the wave, whereas inhibition of the Calvin-Benson cycle accelerated it, (iii) the wave phenomenon was related to the operation of type II NDH (NDH-2). We therefore propose that the wave phenomenon is an important marker of the regulation of electron transport in Symbiodiniaceae.

RevDate: 2023-05-27

Gorshkov AP, Kusakin PG, Borisov YG, et al (2023)

Effect of Triazole Fungicides Titul Duo and Vintage on the Development of Pea (Pisum sativum L.) Symbiotic Nodules.

International journal of molecular sciences, 24(10): pii:ijms24108646.

Triazole fungicides are widely used in agricultural production for plant protection, including pea (Pisum sativum L.). The use of fungicides can negatively affect the legume-Rhizobium symbiosis. In this study, the effects of triazole fungicides Vintage and Titul Duo on nodule formation and, in particular, on nodule morphology, were studied. Both fungicides at the highest concentration decreased the nodule number and dry weight of the roots 20 days after inoculation. Transmission electron microscopy revealed the following ultrastructural changes in nodules: modifications in the cell walls (their clearing and thinning), thickening of the infection thread walls with the formation of outgrowths, accumulation of poly-β-hydroxybutyrates in bacteroids, expansion of the peribacteroid space, and fusion of symbiosomes. Fungicides Vintage and Titul Duo negatively affect the composition of cell walls, leading to a decrease in the activity of synthesis of cellulose microfibrils and an increase in the number of matrix polysaccharides of cell walls. The results obtained coincide well with the data of transcriptomic analysis, which revealed an increase in the expression levels of genes that control cell wall modification and defense reactions. The data obtained indicate the need for further research on the effects of pesticides on the legume-Rhizobium symbiosis in order to optimize their use.

RevDate: 2023-05-27

Koshida K, Ito M, Yakabe K, et al (2023)

Dysfunction of Foxp3[+] Regulatory T Cells Induces Dysbiosis of Gut Microbiota via Aberrant Binding of Immunoglobulins to Microbes in the Intestinal Lumen.

International journal of molecular sciences, 24(10): pii:ijms24108549.

Foxp3[+] regulatory T (Treg) cells prevent excessive immune responses against dietary antigens and commensal bacteria in the intestine. Moreover, Treg cells contribute to the establishment of a symbiotic relationship between the host and gut microbes, partly through immunoglobulin A. However, the mechanism by which Treg cell dysfunction disturbs the balanced intestinal microbiota remains unclear. In this study, we used Foxp3 conditional knockout mice to conditionally ablate the Foxp3 gene in adult mice and examine the relationship between Treg cells and intestinal bacterial communities. Deletion of Foxp3 reduced the relative abundance of Clostridia, suggesting that Treg cells have a role in maintaining Treg-inducing microbes. Additionally, the knockout increased the levels of fecal immunoglobulins and immunoglobulin-coated bacteria. This increase was due to immunoglobulin leakage into the gut lumen as a result of loss of mucosal integrity, which is dependent on the gut microbiota. Our findings suggest that Treg cell dysfunction leads to gut dysbiosis via aberrant antibody binding to the intestinal microbes.

RevDate: 2023-05-27

Bopape FL, Chiulele RM, Shonhai A, et al (2023)

The Genome of a Pigeonpea Compatible Rhizobial Strain '10ap3' Appears to Lack Common Nodulation Genes.

Genes, 14(5): pii:genes14051084.

The symbiotic fixation of atmospheric nitrogen (N) in root nodules of tropical legumes such as pigeonpea (Cajanus cajan) is a complex process, which is regulated by multiple genetic factors at the host plant genotype microsymbiont interface. The process involves multiple genes with various modes of action and is accomplished only when both organisms are compatible. Therefore, it is necessary to develop tools for the genetic manipulation of the host or bacterium towards improving N fixation. In this study, we sequenced the genome of a robust rhizobial strain, Rhizobium tropici '10ap3' that was compatible with pigeonpea, and we determined its genome size. The genome consisted of a large circular chromosome (6,297,373 bp) and contained 6013 genes of which 99.13% were coding sequences. However only 5833 of the genes were associated with proteins that could be assigned to specific functions. The genes for nitrogen, phosphorus and iron metabolism, stress response and the adenosine monophosphate nucleoside for purine conversion were present in the genome. However, the genome contained no common nod genes, suggesting that an alternative pathway involving a purine derivative was involved in the symbiotic association with pigeonpea.

RevDate: 2023-05-27

Beck A, Casanova-Katny A, J Gerasimova (2023)

Metabarcoding of Antarctic Lichens from Areas with Different Deglaciation Times Reveals a High Diversity of Lichen-Associated Communities.

Genes, 14(5): pii:genes14051019.

Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of participants, it is important to know about the accessory organisms and their relationships with various environmental conditions. To this end, we analysed lichen-associated communities from Himantormia lugubris, Placopsis antarctica, P. contortuplicata, and Ramalina terebrata, collected from soils with differing deglaciation times, using a metabarcoding approach. In general, many more Ascomycete taxa are associated with the investigated lichens compared to Basidiomycota. Given our sampling, a consistently higher number of lichen-associated eukaryotes are estimated to be present in areas with deglaciation times of longer than 5000 years compared to more recently deglaciated areas. Thus far, members of Dothideomycetes, Leotiomycetes, and Arthoniomycetes have been restricted to the Placopsis specimens from areas with deglaciation times longer than 5000 years. Striking differences between the associated organisms of R. terebrata and H. lugubris have also been discovered. Thus, a species-specific basidiomycete, Tremella, was revealed for R. terebrata, as was a member of Capnodiales for H. lugubris. Our study provides further understanding of the complex terricolous lichen-associated mycobiome using the metabarcoding approach. It also illustrates the necessity to extend our knowledge of complex lichen symbiosis and further improve the coverage of microbial eukaryotes in DNA barcode libraries, including more extended sampling.

RevDate: 2023-05-27

Duncan SH, Conti E, Ricci L, et al (2023)

Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health.

Biomedicines, 11(5): pii:biomedicines11051338.

A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.

RevDate: 2023-05-27

Ribeiro LEGGT, Batista LDSP, Assis CF, et al (2023)

Potentially Synbiotic Yellow Mombin Beverages: Stability during Refrigerated Storage, Physicochemical Characteristics, and Sensory Properties.

Foods (Basel, Switzerland), 12(10): pii:foods12101994.

This study aimed to develop potentially synbiotic yellow mombin (Spondias mombin L.) beverages added with fructooligosaccharides and Lactiplantibacillus plantarum NRRL B-4496. Six formulations of yellow mombin beverages were prepared to measure the influence of fermentation and pH, which was adjustment to 4.5 for stability and quality parameters. Formulations were evaluated for probiotic survival, pH, titratable acidity, total phenolic compounds (TPC), and antioxidant activity for 28 days at 4 °C. Additionally, the proximate composition, color, sensory aspects, and survival to simulated gastrointestinal conditions were studied. At 21 days of storage, the viability of L. plantarum was 9 CFU/mL for the fermented symbiotic (SYNf) and non-fermented symbiotic with adjusted pH (SYNa) formulations. In addition, the fermented synbiotic with an adjusted pH beverage (SYNfA) showed a count of 8.2 log CFU/mL at 28 days. The formulations showed a high TPC (234-431 mg GAE/L), antioxidant activity (48-75 µM trolox), and a potential use as low-calorie beverages. The SYNf formulation showed an acceptability index higher than 70% and a high purchase intent. The SYNf and SYNa formulations maintained suitable probiotic counts after exposure to the simulated gastrointestinal digestion. Therefore, it was possible to develop a new potentially synbiotic yellow mombin beverage with a high sensory acceptance, supplying the market with a new functional food alternative.

RevDate: 2023-05-27

van Wyk N, Binder J, Ludszuweit M, et al (2023)

The Influence of Pichia kluyveri Addition on the Aroma Profile of a Kombucha Tea Fermentation.

Foods (Basel, Switzerland), 12(10): pii:foods12101938.

Traditional kombucha is a functional tea-based drink that has gained attention as a low or non-alcoholic beverage. The fermentation is conducted by a community of different microorganisms, collectively called SCOBY (Symbiotic Culture of Bacteria and Yeast) and typically consists of different acetic acid bacteria and fermenting yeast, and in some cases lactic acid bacteria that would convert the sugars into organic acids-mostly acetic acid. In this study, the effect of including a Pichia kluyveri starter culture in a kombucha fermentation was investigated. P. kluyveri additions led to a quicker accumulation of acetic acid along with the production of several acetate esters including isoamyl acetate and 2-phenethyl acetate. A subsequent tasting also noted a significant increase in the fruitiness of the kombucha. The significant contribution to the aroma content shows the promise of this yeast in future microbial formulations for kombucha fermentations.

RevDate: 2023-05-27

De Sousa BFS, Domingo-Serrano L, Salinero-Lanzarote A, et al (2023)

The T6SS-Dependent Effector Re78 of Rhizobium etli Mim1 Benefits Bacterial Competition.

Biology, 12(5): pii:biology12050678.

The genes of the type VI secretion system (T6SS) from Rhizobium etli Mim1 (ReMim1) that contain possible effectors can be divided into three modules. The mutants in them indicated that they are not required for effective nodulation with beans. To analyze T6SS expression, a putative promoter region between the tssA and tssH genes was fused in both orientations to a reporter gene. Both fusions are expressed more in free living than in symbiosis. When the module-specific genes were studied using RT-qPCR, a low expression was observed in free living and in symbiosis, which was clearly lower than the structural genes. The secretion of Re78 protein from the T6SS gene cluster was dependent on the presence of an active T6SS. Furthermore, the expression of Re78 and Re79 proteins in E. coli without the ReMim1 nanosyringe revealed that these proteins behave as a toxic effector/immunity protein pair (E/I). The harmful action of Re78, whose mechanism is still unknown, would take place in the periplasmic space of the target cell. The deletion of this ReMim1 E/I pair resulted in reduced competitiveness for bean nodule occupancy and in lower survival in the presence of the wild-type strain.

RevDate: 2023-05-27

Pezzino S, Sofia M, Mazzone C, et al (2023)

Gut Microbiome in the Progression of NAFLD, NASH and Cirrhosis, and Its Connection with Biotics: A Bibliometric Study Using Dimensions Scientific Research Database.

Biology, 12(5): pii:biology12050662.

There is growing evidence that gut microbiota dysbiosis is linked to the etiopathogenesis of nonalcoholic fatty liver disease (NAFLD), from the initial stage of disease until the progressive stage of nonalcoholic steatohepatitis (NASH) and the final stage of cirrhosis. Conversely, probiotics, prebiotics, and synbiotics have shown promise in restoring dysbiosis and lowering clinical indicators of disease in a number of both preclinical and clinical studies. Additionally, postbiotics and parabiotics have recently garnered some attention. The purpose of this bibliometric analysis is to assess recent publishing trends concerning the role of the gut microbiome in the progression of NAFLD, NASH and cirrhosis and its connection with biotics. The free access version of the Dimensions scientific research database was used to find publications in this field from 2002 to 2022. VOSviewer and Dimensions' integrated tools were used to analyze current research trends. Research into the following topics is expected to emerge in this field: (1) evaluation of risk factors which are correlated with the progression of NAFLD, such as obesity and metabolic syndrome; (2) pathogenic mechanisms, such as liver inflammation through toll-like receptors activation, or alteration of short-chain fatty acids metabolisms, which contribute to NAFLD development and its progression in more severe forms, such as cirrhosis; (3) therapy for cirrhosis through dysbiosis reduction, and research on hepatic encephalopathy a common consequence of cirrhosis; (4) evaluation of diversity, and composition of gut microbiome under NAFLD, and as it varies under NASH and cirrhosis by rRNA gene sequencing, a tool which can also be used for the development of new probiotics and explore into the impact of biotics on the gut microbiome; (5) treatments to reduce dysbiosis with new probiotics, such as Akkermansia, or with fecal microbiome transplantation.

RevDate: 2023-05-26

Jeon YJ, Gil CH, Won J, et al (2023)

Symbiotic microbiome Staphylococcus epidermidis restricts IL-33 production in allergic nasal epithelium via limiting the cellular necroptosis.

BMC microbiology, 23(1):154.

BACKGROUND: Allergic rhinitis (AR) is characterized by airway inflammation in nasal mucosa from inhaled allergens and interleukin (IL)-33 is the potent inducer of Th2 inflammation in allergic nasal epithelium. Staphylococcus epidermidis is one of the most abundant colonizers of the healthy human nasal mucosa and might impact the allergen-induced inflammatory responses in the nasal epithelium. Thus, we sought to characterize the mechanism of S. epidermidis regulating Th2 inflammation and IL-33 production in AR nasal mucosa.

RESULTS: The AR symptoms were alleviated and eosinophilic infiltration, serum IgE levels, and Th2 cytokines were significantly decreased in OVA-sensitized AR mice in response to human nasal commensal S. epidermidis. The inoculation of S. epidermidis to normal human nasal epithelial cells reduced IL-33 and GATA3 transcriptions and also reduced IL-33 and GATA3 expression in AR nasal epithelial (ARNE) cells and the nasal mucosa of AR mice. Our data exhibited that the cellular necroptosis of ARNE cells might be involved in IL-33 production and inoculation of S. epidermidis decreased the phosphorylation of necroptosis enzymes in ARNE cells, which was related to the reduction of IL-33 production.

CONCLUSIONS: We present that human nasal commensal S. epidermidis reduces allergic inflammation by suppressing IL-33 production in nasal epithelium. Our findings indicate that S. epidermidis serves a role in blocking allergen-induced cellular necroptosis in allergic nasal epithelium which might be a key mechanism of reduction of IL-33 and Th2 inflammation.

RevDate: 2023-05-26

Chen YP, Li SK, An B, et al (2023)

Effects of arbuscular mycorrhizae and extraradical mycelium of subtropical tree species on soil nitrogen mineralization and enzyme activities.

Ying yong sheng tai xue bao = The journal of applied ecology, 34(5):1235-1243.

Through symbiosis with plants, arbuscular mycorrhizal (AM) fungi effectively improve the availability of soil nitrogen (N). However, the mechanism through which AM and associated extraradical mycelium affect soil N mineralization remains unknow. We carried out an in situ soil culture experiment by using in-growth cores in plantations of three subtropical tree species, Cunninghamia lanceolata, Schima superba, and Liquidambar formosana. We measured soil physical and chemical properties, net N mineralization rate, and the activities of four kinds of hydrolase (leucine aminopeptidase (LAP), β-1,4-N-acetylglucosaminidase (NAG), β-1,4-glucosidase (βG), cellobiohydrolase (CB)) and two kinds of oxidases (polyphenol oxidase (POX) and peroxidase (PER)) involved in soil organic matter (SOM) mineralization in treatments of mycorrhiza (with absorbing roots and hyphae), hyphae (hyphae only), and control (mycorrhiza-free). The results showed that mycorrhizal treatments significantly affected soil total carbon and pH but did not affect N mineralization rates and all enzymatic activities. Tree species significantly affected net ammonification rate, net N mineralization rate and activities of NAG, βG, CB, POX and PER. The net N mineralization rate and enzyme activities in the C. lanceolata stand were significantly higher than that in monoculture broad-leaved stands of either S. superba or L. formosana. There was no interactive effect of mycorrhizal treatment and tree species on any of soil properties, nor on enzymatic activities or net N mineralization rates. Soil pH was negatively and significantly correlated with five kinds of enzymatic activities except for LAP, while net N mineralization rate significantly correlated with ammonium nitrogen content, available phosphorus content, and the activity level of βG, CB, POX, and PER. In conclusion, there was no difference in enzymatic activities and N mineralization rates between rhizosphere and hyphosphere soils of three subtropical tree species in the whole growing season. The activity of particular carbon cycle-related enzymes was closely related to soil N mineralization rate. It is suggested that differences in litter quality and root functional traits among different tree species affect soil enzyme activities and N mineralization rates through organic matter inputs and shaping soil condition.

RevDate: 2023-05-26

Kise H, Nishijima M, Iguchi A, et al (2023)

A new hexactinellid-sponge-associated zoantharian (Porifera, Hexasterophora) from the northwestern Pacific Ocean.

ZooKeys, 1156:71-85 pii:96698.

Symbiotic associations between zoantharians and sponges can be divided into two groups: those that associate with Demospongiae and those that associate with Hexactinellida. Parachurabanashinseimaruae Kise, gen. nov. et sp. nov., a new genus and a new species of Hexactinellida-associated zoantharian from Japanese waters, is described. It is characterized by a combination of the following: i) its host hexactinellid sponge, ii) very flat polyps, iii) cteniform endodermal marginal muscles, and iv) characteristic mutations in three mitochondrial regions (including a unique 26-bp deletion in 16S ribosomal DNA) and three nuclear regions. Parachurabanashinseimaruae Kise, gen. nov. et sp. nov. is the third genus in the family Parazoanthidae that is reported to be associated with Hexasterophora sponges. Although specimens have so far only been collected on Takuyo-Daigo Seamount off Minami-Torishima Island in Japan, unidentified zoantharians of similar description have been reported from the waters around Australia, indicating that the species might be widespread across the Pacific.

RevDate: 2023-05-26

LaPolla JS, SA Schneider (2023)

Trophobiosis between a new species of Acropyga (Hymenoptera, Formicidae) and new Neochavesia (Hemiptera, Xenococcidae) from Peru, and establishment of the Acropygasmithii species-group.

ZooKeys, 1154:1-16 pii:97578.

We describe a new pair of trophobiotic partners from the ant genus Acropyga and the root mealybug genus Neochavesia. A recent field study on Acropyga ants and associated root mealybugs, conducted in the Peruvian Amazon, led to the discovery of Acropygamanuense LaPolla & Schneider, sp. nov. and its root mealybug symbiont Neochavesiapodexuta Schneider & LaPolla, sp. nov. The new root mealybug belongs to the family Xenococcidae, whose members are all obligate associates of Acropyga ants. Providing joint descriptions of new mutualist partners in the same article is a novel approach for this system, and it offers benefits to the ongoing study of mutualism and patterns of association among these symbiotic ants and scales. Here, we also begin to revise the species-group composition of Acropyga by establishing the smithii species-group, and we provide updated information to aid in identifying the new ant species and root mealybug species.

RevDate: 2023-05-26

Ueno Y, S Akimoto (2023)

Long-term light adaptation of light-harvesting and energy-transfer processes in the glaucophyte Cyanophora paradoxa under different light conditions.

Photosynthesis research [Epub ahead of print].

In response to fluctuation in light intensity and quality, oxygenic photosynthetic organisms modify their light-harvesting and excitation energy-transfer processes to maintain optimal photosynthetic activity. Glaucophytes, which are a group of primary symbiotic algae, possess light-harvesting antennas called phycobilisomes (PBSs) consistent with cyanobacteria and red algae. However, compared with cyanobacteria and red algae, glaucophytes are poorly studied and there are few reports on the regulation of photosynthesis in the group. In this study, we examined the long-term light adaptation of light-harvesting functions in a glaucophyte, Cyanophora paradoxa, grown under different light conditions. Compared with cells grown under white light, the relative number of PBSs to photosystems (PSs) increased in blue-light-grown cells and decreased in green-, yellow-, and red-light-grown cells. Moreover, the PBS number increased with increment in the monochromatic light intensity. More energy was transferred from PBSs to PSII than to PSI under blue light, whereas energy transfer from PBSs to PSII was reduced under green and yellow lights, and energy transfer from the PBSs to both PSs decreased under red light. Decoupling of PBSs was induced by intense green, yellow, and red lights. Energy transfer from PSII to PSI (spillover) was observed, but the contribution of the spillover did not distinctly change depending on the culture light intensity and quality. These results suggest that the glaucophyte C. paradoxa modifies the light-harvesting abilities of both PSs and excitation energy-transfer processes between the light-harvesting antennas and both PSs during long-term light adaption.

RevDate: 2023-05-26

D'Agostino PM (2023)

Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria.

Natural product reports [Epub ahead of print].

Covering: up to 2023Cyanobacteria have long been known for their intriguing repertoire of natural product scaffolds, which are often distinct from other phyla. Cyanobacteria are ecologically significant organisms that form a myriad of different symbioses including with sponges and ascidians in the marine environment or with plants and fungi, in the form of lichens, in terrestrial environments. Whilst there have been several high-profile discoveries of symbiotic cyanobacterial natural products, genomic data is scarce and discovery efforts have remained limited. However, the rise of (meta-)genomic sequencing has improved these efforts, emphasized by a steep increase in publications in recent years. This highlight focuses on selected examples of symbiotic cyanobacterial-derived natural products and their biosyntheses to link chemistry with corresponding biosynthetic logic. Further highlighted are remaining gaps in knowledge for the formation of characteristic structural motifs. It is anticipated that the continued rise of (meta-)genomic next-generation sequencing of symbiontic cyanobacterial systems will lead to many exciting discoveries in the future.

RevDate: 2023-05-26

Lauritano C, C Galasso (2023)

Microbial Interactions between Marine Microalgae and Fungi: From Chemical Ecology to Biotechnological Possible Applications.

Marine drugs, 21(5): pii:md21050310.

Chemical interactions have been shown to regulate several marine life processes, including selection of food sources, defense, behavior, predation, and mate recognition. These chemical communication signals have effects not only at the individual scale, but also at population and community levels. This review focuses on chemical interactions between marine fungi and microalgae, summarizing studies on compounds synthetized when they are cultured together. In the current study, we also highlight possible biotechnological outcomes of the synthetized metabolites, mainly for human health applications. In addition, we discuss applications for bio-flocculation and bioremediation. Finally, we point out the necessity of further investigating microalgae-fungi chemical interactions because it is a field still less explored compared to microalga-bacteria communication and, considering the promising results obtained until now, it is worthy of further research for scientific advancement in both ecology and biotechnology fields.

RevDate: 2023-05-26

Ahmad N, Ritz M, Calchera A, et al (2023)

Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.

Journal of fungi (Basel, Switzerland), 9(5): pii:jof9050546.

Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.

RevDate: 2023-05-26

Bento RA, de Novais CB, Saggin-Júnior OJ, et al (2023)

Pioneer Tree Bellucia imperialis (Melastomataceae) from Central Amazon with Seedlings Highly Dependent on Arbuscular Mycorrhizal Fungi.

Journal of fungi (Basel, Switzerland), 9(5): pii:jof9050540.

Bellucia imperialis is one of the most abundant pioneer tree species in anthropized areas of the Central Amazon, and has ecological importance for the environmental resilience of phosphorus (P)-depleted areas. Thus, we investigated whether B. imperialis depends on symbiosis with arbuscular mycorrhizal fungi (AMF) to grow and establish under the edaphic stresses of low nutrient content and low surface moisture retention capacity of the substrate. We tried three AMF inoculation treatments: (1) CON-no mycorrhizae; (2) MIX-with AMF from pure collection cultures, and (3) NAT-with native AMF, combined with five doses of P via a nutrient solution. All CON treatment seedlings died without AMF, showing the high mycorrhizal dependence of B. imperialis. Increasing P doses significantly decreased the leaf area and shoot and root biomass growth for both the NAT and MIX treatments. Increasing P doses did not affect spore number or mycorrhizal colonization, but decreased the diversity of AMF communities. Some species of the AMF community showed plasticity, enabling them to withstand shortages of and excess P. B. imperialis was shown to be sensitive to excess P, promiscuous, dependent on AMF, and tolerant of scarce nutritional resources, highlighting the need to inoculate seedlings to reforest impacted areas.

RevDate: 2023-05-26

Oberemok VV, Gal'chinsky NV, Useinov RZ, et al (2023)

Four Most Pathogenic Superfamilies of Insect Pests of Suborder Sternorrhyncha: Invisible Superplunderers of Plant Vitality.

Insects, 14(5): pii:insects14050462.

Sternorrhyncha representatives are serious pests of agriculture and forestry all over the world, primarily causing damage to woody plants. Sternorrhyncha members are vectors for the transfer of a large number of viral diseases, and subsequently, the host plant weakens. Additionally, many are inherent in the release of honeydew, on which fungal diseases develop. Today, an innovative approach is needed to create new and effective ways to control the number of these insects based on environmentally friendly insecticides. Of particular relevance to such developments is the need to take into account the large number of organisms living together with insect pests in this group, including beneficial insects. Practically without changing their location on their host plant, they adopted to be more invisible and protected due to their small size, symbiosis with ants, the ability to camouflage with a leaf, and moderately deplete plants and others, rarely leading them to death but still causing substantial economic loss in the subtropics and tropics. Due to the lack of presence in the literature, this review fills in this pesky spot by examining (on the example of distinct species from four superfamilies) the characteristic adaptations for this suborder and the chemical methods of combating these insects that allow them to survive in various environmental conditions, suggesting new and highly promising ways of using olinscides for plant protection against Sternorrhyncha members.

RevDate: 2023-05-26

Chou PA, Bain A, Chantarasuwan B, et al (2023)

Parasitism Features of a Fig Wasp of Genus Apocrypta (Pteromalidae: Pteromalinae) Associated with a Host Belonging to Ficus Subgenus Ficus.

Insects, 14(5): pii:insects14050437.

Non-pollinating fig wasps (NPFWs), particularly long-ovipositored Sycoryctina wasps, exhibit a high species specificity and exert complex ecological effects on the obligate mutualism between the plant genus Ficus and pollinating fig wasps. Apocrypta is a genus of NPFWs that mostly interacts with the Ficus species under the subgenus Sycomorus, and the symbiosis case between Apocrypta and F. pedunculosa var. mearnsii, a Ficus species under subgenus Ficus, is unique. As fig's internal environments and the wasp communities are distinct between the two subgenera, we addressed the following two questions: (1) Are the parasitism features of the Apocrypta wasp associated with F. pedunculosa var. mearnsii different from those of other congeneric species? (2) Is this Apocrypta species an efficient wasp that lives in its unique host? Our observation revealed that this wasp is an endoparasitic idiobiont parasitoid, as most congeneric species are, but developed a relatively long ovipositor. Furthermore, the relationships of the parasitism rate versus the pollinator number, the fig wall, and the sex ratio of the pollinator, respectively, showed that it possessed a higher parasitism ability than that of other congeners. However, its parasitism rate was low, and thus it was not an efficient wasp in its habitat. This difference between parasitism ability and parasitism rate might be a consequence of its oviposition strategy and the severe habitat conditions. These findings may also provide insights into the mechanism to maintain the interaction between the fig tree and the fig wasp community.

RevDate: 2023-05-26

Huang Q, Feng Y, Shan HW, et al (2023)

A Novel Nitrogen-Fixing Bacterium Raoultella electrica Isolated from the Midgut of the Leafhopper Recilia dorsalis.

Insects, 14(5): pii:insects14050431.

Nitrogen is a crucial element for the growth and development of insects, but herbivorous insects often suffer from nitrogen nutrition deficiencies in their diets. Some symbiotic microorganisms can provide insect hosts with nitrogen nutrition through nitrogen fixation. Extensive research has clearly demonstrated the process of nitrogen fixation by symbiotic microorganisms in termites, while evidence supporting the occurrence and significance of nitrogen fixation in the diets of the Hemiptera is less conclusive. In this study, we isolated a strain of R. electrica from the digestive tract of a leafhopper, R. dorsalis, and found that it had nitrogen-fixing capabilities. Fluorescence in situ hybridization results showed that it was located in the gut of the leafhopper. Genome sequencing revealed that R. electrica possessed all the genes required for nitrogen fixation. We further evaluated the growth rate of R. electrica in nitrogen-containing and nitrogen-free media and measured its nitrogenase activity through an acetylene reduction assay. The findings of these studies could shed light on how gut microbes contribute to our understanding of nitrogen fixation.

RevDate: 2023-05-26

Wei Y, Su Y, Han X, et al (2023)

Evaluation of Transgenerational Effects of Sublethal Imidacloprid and Diversity of Symbiotic Bacteria on Acyrthosiphon gossypii.

Insects, 14(5): pii:insects14050427.

Symbiotic bacteria and hormesis in aphids are the driving forces for pesticide resistance. However, the mechanism remains unclear. In this study, the effects of imidacloprid on the population growth parameters and symbiotic bacterial communities of three successive generations of Acyrthosiphon gossypii were investigated. The bioassay results showed that imidacloprid had high toxicity to A. gossypii with an LC50 of 1.46 mg·L[-1]. The fecundity and longevity of the G0 generation of A. gossypii decreased when exposed to the LC15 of imidacloprid. The net reproductive rate (R0), intrinsic rate of increase (rm), finite rate of increase (λ), and total reproductive rate (GRR) of G1 and G2 offspring were significantly increased, but those of the control and G3 offspring were not. In addition, sequencing data showed that the symbiotic bacteria of A. gossypii mainly belonged to Proteobacteria, with a relative abundance of 98.68%. The dominant genera of the symbiotic bacterial community were Buchnera and Arsenophonus. After treatment with the LC15 of imidacloprid, the diversity and species number of bacterial communities of A. gossypii decreased for G1-G3 and the abundance of Candidatus-Hamiltonella decreased, but Buchnera increased. These results provide insight into the resistance mechanism of insecticides and the stress adaptation between symbiotic bacteria and aphids.

RevDate: 2023-05-26

Li Y, Bi M, Sun S, et al (2023)

Comparative metabolomic profiling reveals molecular mechanisms underlying growth promotion and disease resistance in wheat conferred by Piriformospora indica in the field.

Plant signaling & behavior, 18(1):2213934.

Piriformospora indica, a plant root-colonizing basidiomycete fungus, exhibits strong growth-promoting activity in symbiosis with a broad range of plants. Here, we report the potential of P. indica to improve growth, yield, and disease resistance in wheat in the field. In the present study, P. indica successfully colonized wheat through chlamydospores and formed dense mycelial networks that covered roots. Plants subjected to the seed soaking (SS) treatment with P. indica chlamydospore suspensions enhanced tillering 2.28-fold compared to the non-inoculated wheat in the tillering stage. In addition, P. indica colonization promoted vegetative growth significantly during the three-leaf, tillering, and jointing stages. Moreover, the P. indica-SS-treatment enhanced wheat yield by 16.37 ± 1.63%, by increasing grains per ear and panicle weight and decreased damage to wheat shoot and root architecture markedly, with high field control effects against Fusarium pseudograminearum (81.59 ± 1.32%), Bipolaris sorokiniana (82.19 ± 1.59%), and Rhizoctonia cerealis (75.98 ± 1.36%). Most of the primary metabolites, such as amino acids, nucleotides, and lipids, involved in vegetative reproduction were increased in P. indica-SS-treatment plants, whereas secondary metabolites, such as terpenoids, polyketides, and alkaloids, decreased following P. indica inoculation. The up-regulated processes of protein, carbohydrate, and lipid metabolism indicated that P. indica colonization increased growth, yield, and disease resistance via the acceleration of plant primary metabolism. In conclusion, P. indica improved morphological, physiological, and metabolic substance levels, and further promoted its growth, yield, and disease resistance in wheat.

RevDate: 2023-05-25

John SA, JG Ray (2023)

Optimization of environmental and the other variables in the application of arbuscular mycorrhizal fungi as an ecotechnological tool for sustainable paddy cultivation: A critical review.

Journal of applied microbiology pii:7179989 [Epub ahead of print].

Arbuscular Mycorrhizal Fungi (AMF) are effective natural alternatives to assist plants in improving crop productivity and immunity against pests and diseases. However, a comprehensive idea of the variables under which they show optimum activity, especially concerning particular soil, climate, geography, and crop characteristics, has yet to be adequately standardized. Since paddy is the staple food for half of the world's population, such standardization is highly significant globally. Research concerning determinants affecting AMF functioning in rice is limited. However, the identified variables include external variables such as abiotic, biotic, and anthropogenic factors and internal variables such as plant and AMF characteristics. Among the abiotic factors, edaphic factors like soil pH, phosphorus availability, and soil moisture significantly affect AMF functioning in rice. In addition, anthropogenic influences such as land use patterns, flooding, and fertilizer regimes also affect AMF communities in rice agroecosystems. The principal objective of the review was to analyse the existing literature on AMF concerning such variables generally and to assess the specific research requirements on variables affecting AMF in rice. The ultimate goal is to identify research gaps for applying AMF as a natural alternative in the sustainable agriculture of paddy with optimum AMF symbiosis enhancing rice productivity.

RevDate: 2023-05-25

Mandal M, Das S, Roy A, et al (2023)

Interactive relations between plants, phyllosphere microbial community, and particulate matter pollution.

The Science of the total environment pii:S0048-9697(23)02973-X [Epub ahead of print].

Particulate matter (PM) pollution poses a significant risk to many ecosystems; as sessile organisms, plants are at particular risk from PM pollution since they cannot move away from it. Microorganisms are essential components of ecosystems that can help macro-organisms to cope with pollutants (such as PM). In the phyllosphere (the aerial/above-ground parts of plants colonized by microbial communities), plant-microbe associations have been found to promote plant development while also increasing host resilience to biotic and abiotic stressors. This review discusses how plant-microbe symbiosis in the phyllosphere potentially affects host survivability and efficiency in the face of pollution and factors such as climate change. Evidence is presented that plant-microbe associations can be beneficial, such as by degrading pollutants, yet also bring disadvantages, such as causing the loss of symbiotic organisms and/or inducing disease. It is suggested that plant genetics is a fundamental driver of the phyllosphere microbiome assembly, connecting phyllosphere microbiota to plant health management in adverse conditions. Finally, potential ways that essential community ecological processes might influence plant-microbe partnerships in the face of Anthropocene-linked changes and what this might mean for environmental management are discussed.

RevDate: 2023-05-25

Mohan A, Godugu S, Joshi SS, et al (2023)

Gut-brain axis: altered microbiome and depression - review.

Annals of medicine and surgery (2012), 85(5):1784-1789.

The concept of a 'gut-brain axis' was recently developed when the complex communications between the brain and the gut became evident. The interaction may affect emotions, motivation, mood, and higher cognitive functions as well as gut homeostasis. Human microbe symbiosis's merits are now acknowledged to transcend human mental health. Research has recently indicated that the gut-brain axis plays a vital role in brain health maintenance. The term 'gut-brain axis' can only partially capture the intricacy of these interactions. Dysbiosis of the gut commensals has been seen in patients with psychiatric diseases, such as depression. Major depressive disorder is caused by complicated interactions between the individual gene and the environment. In a forced swimming test, P. Zheng et al. discovered that germ-free mice with no gut microbiota had a shorter immobility duration than healthy mice. More radical effects were expressed on the use of probiotics rather than prebiotics and postbiotics in reducing the symptoms of depression in patients with major depressive disorder. One of prime importance can be given to exploring more microbiota to investigate the better therapeutic effects of probiotics, prebiotics, and postbiotics.

RevDate: 2023-05-25

Suo Z, Cummings DA, Puri AW, et al (2023)

A Mesorhizobium japonicum quorum sensing circuit that involves three linked genes and an unusual acyl-homoserine lactone signal.

mBio [Epub ahead of print].

Members of the genus Mesorhizobium, which are core components of the rhizosphere and specific symbionts of legume plants, possess genes for acyl-homoserine lactone (AHL) quorum sensing (QS). Here we show Mesorhizobium japonicum MAFF 303099 (formerly M. loti) synthesizes and responds to N-[(2E, 4E)-2,4-dodecadienoyl] homoserine lactone (2E, 4E-C12:2-HSL). We show that the 2E, 4E-C12:2-HSL QS circuit involves one of four luxR-luxI-type genes found in the sequenced genome of MAFF 303099. We refer to this circuit, which appears to be conserved among Mesorhizobium species, as R1-I1. We show that two other Mesorhizobium strains also produce 2E, 4E-C12:2-HSL. The 2E, 4E-C12:2-HSL is unique among known AHLs in its arrangement of two trans double bonds. The R1 response to 2E, 4E-C12:2-HSL is extremely selective in comparison with other LuxR homologs, and the trans double bonds appear critical for R1 signal recognition. Most well-studied LuxI-like proteins use S-adenosylmethionine and an acyl-acyl carrier protein as substrates for synthesis of AHLs. Others that form a subgroup of LuxI-type proteins use acyl-coenzyme A substrates rather than acyl-acyl carrier proteins. I1 clusters with the acyl-coenzyme A-type AHL synthases. We show that a gene linked to the I1 AHL synthase is involved in the production of the QS signal. The discovery of the unique I1 product enforces the view that further study of acyl-coenzyme A-dependent LuxI homologs will expand our knowledge of AHL diversity. The involvement of an additional enzyme in AHL generation leads us to consider this system a three-component QS circuit.IMPORTANCEWe report a Mesorhizobium japonicum quorum sensing (QS) system involving a novel acyl-homoserine lactone (AHL) signal. This system is known to be involved in root nodule symbiosis with host plants. The chemistry of the newly described QS signal indicated that there may be a dedicated cellular enzyme involved in its synthesis in addition to the types known for production of other AHLs. Indeed, we report that an additional gene is required for synthesis of the unique signal, and we propose that this is a three-component QS circuit as opposed to the canonical two-component AHL QS circuits. The signaling system is exquisitely selective. The selectivity may be important when this species resides in the complex microbial communities around host plants and may make this system useful in various synthetic biology applications of QS circuits.

RevDate: 2023-05-25

Medina JM, Queller DC, Strassmann JE, et al (2023)

The social amoeba dictyostelium discoideum rescues paraburkholderia hayleyella, but not P. agricolaris, from interspecific competition.

FEMS microbiology ecology pii:7179410 [Epub ahead of print].

Bacterial endosymbionts can provide benefits for their eukaryotic hosts, but it is often unclear if endosymbionts benefit from these relationships. The social amoeba Dictyostelium discoideum associates with three species of Paraburkholderia endosymbionts, including P. agricolaris and P. hayleyella. These endosymbionts can be costly to host but are beneficial in certain contexts because they allow D. discoideum to carry prey bacteria through the dispersal stage. In experiments where no other species are present, P. hayleyella benefits from D. discoideum while P. agricolaris does not. However, the presence of other species may influence this symbiosis. We tested if P. agricolaris and P. hayleyella benefit from D. discoideum in the context of resource competition with Klebsiella pneumoniae, the typical laboratory prey of D. discoideum. Without D. discoideum, K. pneumoniae depressed the growth of both Paraburkholderia symbionts, consistent with competition. P. hayleyella was more harmed by interspecific competition than P. agricolaris. We found that P. hayleyella was rescued from competition by D. discoideum while P. agricolaris was not. This may be because P. hayleyella is more specialized as an endosymbiont; it has a highly reduced genome compared to P. agricolaris and may have lost genes relevant for resource competition outside of its host.

RevDate: 2023-05-24

Ji Y, Huang L, Wang Z, et al (2023)

Performance of cocultivation of Chlorella vulgaris and four different fungi in biogas slurry purification and biogas upgrading by induction of strigolactone (GR24) and endophytic bacteria.

This study aimed to determine the best fungi to form the algal-bacterial-fungal symbionts and identify the optimal conditions for the synchronous processing of biogas slurry and biogas. Chlorella vulgaris (C. vulgaris) and endophytic bacteria (S395-2) isolated from it and four different fungi (Ganoderma lucidum, Pleurotus ostreatus, Pleurotus geesteranus, and Pleurotus corucopiae) were used to form different symbiotic systems. Four different concentrations of GR24 were added to systems to examine the growth characteristics, the content of chlorophyll a (CHL-a), the activity of carbonic anhydrase (CA), the photosynthetic performance, the removal of nutrients, and the biogas purification performance. The results suggested that the growth rate, CA, CHL-a content, and photosynthetic performance of the C. vulgaris-endophytic bacteria-Ganoderma lucidum symbionts were higher than the other three symbiotic systems when 10[-9] M GR24 was added. The highest nutrients/CO2 removal efficiency 78.36 ± 6.98% for chemical oxygen demand (COD), 81.63 ± 7.35% for total nitrogen (TN), 84.05 ± 7.16% for total phosphorus (TP) and 65.18 ± 6.12% for CO2 was obtained under the above optimal conditions. This approach will provide a theoretical basis for the selection and optimization of the algal-bacterial-fungal symbionts for biogas slurry and biogas purification.

RevDate: 2023-05-24

McFadden CL (2023)

Social media for health advocacy.

Surgery pii:S0039-6060(23)00245-3 [Epub ahead of print].

Twenty-five percent of US adults do not have a primary care doctor. With inherent physical obstacles often found in health care systems, there is a disparity in the ability to navigate through health care. Social media has helped patients navigate the muddy waters and helped remove traditional medicine's roadblocks, which tend to limit access to health care resources. Through social media, patients access areas to promote health, network and build their communities, and become better advocates to make more informed health care decisions. However, limitations exist for health advocacy through social media, including widespread medical misinformation, disregard of evidence-based practices, and challenges to ensure user privacy. Regardless of the limitations, the medical community must accept and work with medical professional societies to stay at the forefront of shared material and become interwoven in social media. This engagement could help empower the public with knowledge to advocate for themselves and know where to go for definitive medical care when warranted. Medical professionals must embrace the public's research and self-advocacy as the foundation of a new symbiotic relationship.

RevDate: 2023-05-24

Pu Z, Zhang R, Wang H, et al (2023)

Root morphological and physiological traits and arbuscular mycorrhizal fungi shape phosphorus-acquisition strategies of 12 vegetable species.

Frontiers in plant science, 14:1150832.

Trait plasticity and integration mediate vegetable adaptive strategies. However, it is unclear how patterns of vegetables in root traits influence vegetable adaptation to different phosphorus (P) levels. Nine root traits and six shoot traits were investigated in 12 vegetable species cultivated in a greenhouse with low and high P supplies to identify distinct adaptive mechanisms in relation to P acquisition (40 and 200 P mg kg[-1] as KH2PO4). At the low P level, a series of negative correlations among root morphology, exudates and mycorrhizal colonization, and different types of root functional properties (root morphology, exudates and mycorrhizal colonization) respond differently to soil P levels among vegetable species. non-mycorrhizal plants showed relatively stable root traits as compared to solanaceae plants that showed more altered root morphologies and structural traits. At the low P level, the correlation between root traits of vegetable crops was enhanced. It was also found in vegetables that low P supply enhances the correlation of morphological structure while high P supply enhances the root exudation and the correlation between mycorrhizal colonization and root traits. Root exudation combined with root morphology and mycorrhizal symbiosis to observe P acquisition strategies in different root functions. Vegetables respond highly under different P conditions by enhancing the correlation of root traits. Low P supply could significantly improve the direct and indirect ways of mycorrhizal vegetable crops' root traits axis on shoot biomass, and enhance the direct way of non-mycorrhizal vegetable crops' root traits axis and reduce the indirect way of root exudates.

RevDate: 2023-05-24

Wilkes TI (2023)

Ergosterol extraction: a comparison of methodologies.

Access microbiology, 5(4):.

Ergosterol is a component of the cell membrane of mycorrhizal fungi and is frequently used to quantify their biomass. Arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (ECM) fungi establish a symbiotic relationship with a respective host plant. Several methods are currently employed for quantification of ergosterol; however, these utilise a series of potentially hazardous chemicals with varying exposure times to the user. The present comparative study aims to ascertain the most reliable method to extract ergosterol whilst limiting hazard exposure to the user. Chloroform, cyclohexane, methanol and methanol hydroxide extraction protocols were applied to a total of 300 samples of root samples and a further 300 growth substrate samples across all protocols. Extracts were analysed via HPLC methodologies. Chromagraphic analysis showed chloroform-based extraction procedures produced a consistently higher concentration of ergosterol in both root and growth substrate samples. Methanol hydroxide, without the addition of cyclohexane, produced a very low concentration of ergosterol, with a reduction of quantified ergosterol of between 80 and 92 % compared to chloroform extractions. Hazard exposure was greatly reduced following the chloroform extraction protocol when compared with other extraction procedures.

RevDate: 2023-05-24

Schmiedová L, Černá K, Li T, et al (2023)

Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time.

International microbiology : the official journal of the Spanish Society for Microbiology [Epub ahead of print].

Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.

RevDate: 2023-05-24

Kaboosi E, Ghabooli M, R Karimi (2023)

Combined Effect of Trehalose and Serendipita indica Inoculation Might Participate in Solanum lycopersicum Induced Cold Tolerance.

Current microbiology, 80(7):224.

The exploitation of symbiotic interactions between fungi and plants, coupled with the application of osmoprotectants such as trehalose (Tre), presents a promising strategy for mitigating environmental stress. To determine the mechanism of Serendipita indica and Tre-mediated cold stress tolerance, a comparative experiment was designed to study the impact of S. indica, Tre and their combination on tomato plants grown under cold stress. The results showed that cold stress significantly decreased biomass, relative water content, photosynthetic pigments and elements concomitantly with increasing antioxidant activities, malondialdehyde (MDA), electrolyte leakage, hydrogen peroxide and proline content. Meanwhile, S. indica and Tre treatments promoted biomass and enhanced carbohydrate, protein, proline, potassium, phosphorous, antioxidant enzymes and photosynthetic pigments content under cold stress. Furthermore, single or dual application of endophyte and Tre mitigated physiological disorders induced by cold stress and increased the integrity of cell membranes by decreasing hydrogen peroxide, MDA, and electrolyte leakage (EL). Our findings suggest that S. indica and Tre combination could significantly promote cold stress tolerance compared with single treatment. This study is novel in showing the cold adaptation of tomato plants by combination use of S. indica and Tre, which can be a promising strategy for improving cold tolerance. The underlying molecular mechanisms of sugar-fungus interaction must be further investigated.

RevDate: 2023-05-24

Xu D, Yu X, Chen J, et al (2023)

Microbial Assemblages Associated with the Soil-Root Continuum of an Endangered Plant, Helianthemum songaricum Schrenk.

Microbiology spectrum [Epub ahead of print].

The microbial network of the soil-root continuum plays a key role in plant growth. To date, limited information is available about the microbial assemblages in the rhizosphere and endosphere of endangered plants. We suspect that unknown microorganisms in roots and soil play an important role in the survival strategies of endangered plants. To address this research gap, we investigated the diversity and composition of the microbial communities of the soil-root continuum of the endangered shrub Helianthemum songaricum and observed that the microbial communities and structures of the rhizosphere and endosphere samples were distinguishable. The dominant rhizosphere bacteria were Actinobacteria (36.98%) and Acidobacteria (18.15%), whereas most endophytes were Alphaproteobacteria (23.17%) as well as Actinobacteria (29.94%). The relative abundance of rhizosphere bacteria was higher than that in endosphere samples. Fungal rhizosphere and endophyte samples had approximately equal abundances of the Sordariomycetes (23%), while the Pezizomycetes were more abundant in the soil (31.95%) than in the roots (5.70%). The phylogenetic relationships of the abundances of microbes in root and soil samples also showed that the most abundant bacterial and fungal reads tended to be dominant in either the soil or root samples but not both. Additionally, Pearson correlation heatmap analysis showed that the diversity and composition of soil bacteria and fungi were closely related to pH, total nitrogen, total phosphorus, and organic matter, of which pH and organic matter were the main drivers. These results clarify the different patterns of microbial communities of the soil-root continuum, in support of the better conservation and utilization of endangered desert plants in Inner Mongolia. IMPORTANCE Microbial assemblages play significant roles in plant survival, health, and ecological services. The symbiosis between soil microorganisms and these plants and their interactions with soil factors are important features of the adaptation of desert plants to an arid and barren environment. Therefore, the profound study of the microbial diversity of rare desert plants can provide important data to support the protection and utilization of rare desert plants. Accordingly, in this study, high-throughput sequencing technology was applied to study the microbial diversity in plant roots and rhizosphere soils. We expect that research on the relationship between soil and root microbial diversity and the environment will improve the survival of endangered plants in this environment. In summary, this study is the first to study the microbial diversity and community structure of Helianthemum songaricum Schrenk and compare the diversity and composition of the root and soil microbiomes.

RevDate: 2023-05-23

Chaudhary S, Wu Y, Strongman D, et al (2023)

CIGAF-a database and interactive platform for insect-associated trichomycete fungi.

Database : the journal of biological databases and curation, 2023:.

Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.

RevDate: 2023-05-23

Carr EC, Barton Q, Grambo S, et al (2023)

Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche.

G3 (Bethesda, Md.) pii:7176444 [Epub ahead of print].

Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primarily yeast form. These fungi grow in xeric, nutrient deplete environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community is not well understood. We have isolated two novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e., E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin that can potentially provide UV resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.

RevDate: 2023-05-23

Haruma T, Doyama K, Lu X, et al (2023)

Miscanthus sinensis contributes to the survival of Pinus densiflora seedlings at a mining site via providing a possible functional endophyte and maintaining symbiotic relationship between P. densiflora and endophytes from high soil temperature stress.

PloS one, 18(5):e0286203 pii:PONE-D-22-32352.

At a sedimentary site in an old mine site, Miscanthus sinensis formed patches, where Pinus densiflora seedlings could grow better compared with those outside the patches, indicating that M. sinensis would improve P. densiflora seedling establishment. The purpose of this study was to understand the mechanisms by which M. sinensis facilitates the survival of P. densiflora seedlings by considering the soil properties, heavy metal tolerance, and root endophytes in P. densiflora seedlings at the sedimentary site. The sedimentary site, which is a bare ground, contained high concentrations of Fe, indicating that plants should be exposed to Fe and high soil temperature stresses. Measurement of soil temperature revealed that M. sinensis suppressed sharp increases and alternation of soil temperature, resulting in reducing high soil temperature stress in P. densiflora seedlings. To adapt to the Fe stress environment, P. densiflora outside and inside the patches produced Fe detoxicants, including catechin, condensed tannin, and malic acid. Ceratobasidium bicorne and Aquapteridospora sp. were commonly isolated from P. densiflora seedlings outside and inside the patches as root endophytes, which might enhance Fe tolerance in the seedlings. Aquapteridospora sp., which is considered as a dark-septate endophyte (DSE), was also isolated from the roots of M. sinensis, suggesting that M. sinensis might play a source of a root endophyte to P. densiflora seedlings. Ceratobasidium bicorne could be classified into root endophytes showing symbiosis and weak pathogenicity to host plants. Therefore, high soil temperature stress would weaken P. densiflora seedlings, causing root endophytic C. bicorne to appear pathogenic. We suggested that P. densiflora could adapt to the Fe stress environment via producing Fe detoxicants, and M. sinensis would facilitate the establishment of P. densiflora seedlings in the sedimentary site by providing a DSE, Aquapteridospora sp., and maintaining symbiosis of C. bicorne from high soil temperature stress.

RevDate: 2023-05-22

Cai J, Muhammad I, Chen B, et al (2023)

Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata.

BMC genomics, 24(1):275.

BACKGROUND: Armillaria species are plant pathogens, but a few Armillaria species can establish a symbiotic relationship with Gastrodia elata, a rootless and leafless orchid, that is used as a Chinese herbal medicine. Armillaria is a nutrient source for the growth of G. elata. However, there are few reports on the molecular mechanism of symbiosis between Armillaria species and G. elata. The genome sequencing and analysis of Armillaria symbiotic with G. elata would provide genomic information for further studying the molecular mechanism of symbiosis.

RESULTS: The de novo genome assembly was performed with the PacBio Sequel platform and Illumina NovaSeq PE150 for the A. gallica Jzi34 strain, which was symbiotic with G. elata. Its genome assembly contained ~ 79.9 Mbp and consisted of 60 contigs with an N50 of 2,535,910 bp. There were only 4.1% repetitive sequences in the genome assembly. Functional annotation analysis revealed a total of 16,280 protein coding genes. Compared with the other five genomes of Armillaria, the carbohydrate enzyme gene family of the genome was significantly contracted, while it had the largest set of glycosyl transferase (GT) genes. It also had an expansion of auxiliary activity enzymes AA3-2 gene subfamily and cytochrome P450 genes. The synteny analysis result of P450 genes reveals that the evolutionary relationship of P450 proteins between A. gallica Jzi34 and other four Armillaria was complex.

CONCLUSIONS: These characteristics may be beneficial for establishing a symbiotic relationship with G. elata. These results explore the characteristics of A. gallica Jzi34 from a genomic perspective and provide an important genomic resource for further detailed study of Armillaria. This will help to further study the symbiotic mechanism between A. gallica and G. elata.

RevDate: 2023-05-22

Wang J, Gao L, S Aksoy (2023)

Microbiota in disease-transmitting vectors.

Nature reviews. Microbiology [Epub ahead of print].

Haematophagous arthropods, including mosquitoes, ticks, flies, triatomine bugs and lice (here referred to as vectors), are involved in the transmission of various pathogens to mammals on whom they blood feed. The diseases caused by these pathogens, collectively known as vector-borne diseases (VBDs), threaten the health of humans and animals. Although the vector arthropods differ in life histories, feeding behaviour as well as reproductive strategies, they all harbour symbiotic microorganisms, known as microbiota, on which they depend for completing essential aspects of their biology, such as development and reproduction. In this Review, we summarize the shared and unique key features of the symbiotic associations that have been characterized in the major vector taxa. We discuss the crosstalks between microbiota and their arthropod hosts that influence vector metabolism and immune responses relevant for pathogen transmission success, known as vector competence. Finally, we highlight how current knowledge on symbiotic associations is being explored to develop non-chemical-based alternative control methods that aim to reduce vector populations, or reduce vector competence. We conclude by highlighting the remaining knowledge gaps that stand to advance basic and translational aspects of vector-microbiota interactions.

RevDate: 2023-05-22

Li Z, Yang M, Zhou X, et al (2023)

Research on the spatial correlation and formation mechanism between traditional villages and rural tourism.

Scientific reports, 13(1):8210.

In recent years, the survival and development of traditional villages in China have been serious challenges. Rural tourism is regarded as an important way to solve rural problems, and the combination of rural culture and tourism has become a new power point for rural development. Therefore, it is necessary to explore the spatial distribution structure between traditional villages and rural tourism. In this paper, rural tourism was represented by the rural tourism characteristic village (RTCV), and Henan Province, China, was taken as a study area to analyze the distribution pattern and spatial correlation of rural tourism and traditional village (TV) and discuss the relationship between the spatial correlation and regional natural environment and socioeconomic factors. The results show that the coupling of the spatial correlation between RTCVs and TVs in Henan was clear. They could be divided into 5 regions based on geographical factors. In addition, the research summarized 4 typical spatial structures between TVs and RTCVs in Henan based on the regional symbiosis theory, and the spatial pattern formation mechanism of TVs and RTCVs was discussed based on three driving mechanisms. The spatial structure of the two can provide reference value for other developing countries and regions to achieve sustainable rural development.

RevDate: 2023-05-22

Liu XF, Shao JH, Liao YT, et al (2023)

Regulation of short-chain fatty acids in the immune system.

Frontiers in immunology, 14:1186892.

A growing body of research suggests that short-chain fatty acids (SCFAs), metabolites produced by intestinal symbiotic bacteria that ferment dietary fibers (DFs), play a crucial role in the health status of symbiotes. SCFAs act on a variety of cell types to regulate important biological processes, including host metabolism, intestinal function, and immune function. SCFAs also affect the function and fate of immune cells. This finding provides a new concept in immune metabolism and a better understanding of the regulatory role of SCFAs in the immune system, which impacts the prevention and treatment of disease. The mechanism by which SCFAs induce or regulate the immune response is becoming increasingly clear. This review summarizes the different mechanisms through which SCFAs act in cells. According to the latest research, the regulatory role of SCFAs in the innate immune system, including in NLRP3 inflammasomes, receptors of TLR family members, neutrophils, macrophages, natural killer cells, eosinophils, basophils and innate lymphocyte subsets, is emphasized. The regulatory role of SCFAs in the adaptive immune system, including in T-cell subsets, B cells, and plasma cells, is also highlighted. In addition, we discuss the role that SCFAs play in regulating allergic airway inflammation, colitis, and osteoporosis by influencing the immune system. These findings provide evidence for determining treatment options based on metabolic regulation.

RevDate: 2023-05-22

Moldovan OT, Carrell AA, Bulzu PA, et al (2023)

The gut microbiome mediates adaptation to scarce food in Coleoptera.

bioRxiv : the preprint server for biology pii:2023.05.12.540564.

Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibulae adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia . All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.

RevDate: 2023-05-22

Mfopit YM, Weber JS, Chechet GD, et al (2023)

Molecular detection of Sodalis glossinidius, Spiroplasma and Wolbachia endosymbionts in wild population of tsetse flies collected in Cameroon, Chad and Nigeria.

Research square pii:rs.3.rs-2902767.

Background Tsetse flies are cyclical vectors of African trypanosomiasis. They have established symbiotic associations with different bacteria, which influence certain aspects of their physiology. The vector competence of tsetse flies for different trypanosome species is highly variable and is suggested to be affected by various factors, amongst which are bacterial endosymbionts. Symbiotic interactions may provide an avenue for the disease control. The current study provided the prevalence of 3 tsetse symbionts in Glossina species from Cameroon, Chad and Nigeria. Results Tsetse flies were collected from five different locations and dissected. DNA was extracted and polymerase chain reaction PCR was used to detect the presence of Sodalis glossinidius , Spiroplasma sp and Wolbachia using specific primers. A total of 848 tsetse samples were analysed: Glossina morsitans submorsitans (47.52%), Glossina palpalis palpalis (37.26%), Glossina fuscipes fuscipes (9.08%) and Glossina tachinoides (6.13%). Only 95 (11.20%) were infected with at least one of the 3 symbionts. Among the infected, 6 (6.31%) were carrying mixed infection (Wolbachia and Spiroplasma). The overall symbiont prevalence was 0.88%, 3.66% and 11.00% respectively, for Sodalis , Spiroplasma and Wolbachia . Prevalence varied between countries and tsetse species. No Spiroplasma was detected in samples from Cameroon and no Sodalis was found in samples from Nigeria. Conclusion The present study revealed for the first time, the presence of infection by Spiroplasma in tsetse in Chad and Nigeria. These findings provide useful information to the repertoire of bacterial flora of tsetse flies and incite to more investigations to understand their implication in the vector competence of tsetse flies.

RevDate: 2023-05-22

Williamson OM, Mustard AT, Bright AJ, et al (2023)

Opportunistic consumption of coral spawn by the ruby brittle star (Ophioderma rubicundum).

Ecology and evolution, 13(5):e10096 pii:ECE310096.

Many reef invertebrates reproduce through simultaneous broadcast spawning, with an apparent advantage of overwhelming potential predators and maximizing propagule survival. Although reef fish have been observed to consume coral gamete bundles during spawning events, there are few records of such predation by benthic invertebrates. Here, we document several instances of the ruby brittle star, Ophioderma rubicundum, capturing and consuming egg-sperm bundles of the mountainous star coral, Orbicella faveolata, and the symmetrical brain coral, Pseudodiploria strigosa, during spawning events in the Cayman Islands in 2012 and the Florida Keys in 2022. These observations are widely separated in space and time (>600 km, 10 years), suggesting that this behavior may be prevalent on western Atlantic reefs. Since O. rubicundum spawns on the same or subsequent nights as these coral species, we hypothesize that this opportunistic feeding behavior takes advantage of lipid-rich coral gamete bundles to recover energy reserves expended by the brittle star during gametogenesis. The consumption of coral gametes by adult brittle stars suggests an underexplored trophic link between reef invertebrates and also provides evidence that ophiuroid-coral symbioses may oscillate between commensalism and parasitism depending on the ontogeny and reproductive status of both animals. Our observations provide insights into the nuanced, dynamic associations between coral reef invertebrates and may have implications for coral reproductive success and resilience.

RevDate: 2023-05-22

Ubuka T, Bu G, Y Tobari (2023)

Editorial: Stress and reproduction in animal models.

Frontiers in endocrinology, 14:1202275.

RevDate: 2023-05-22

Chin T, Shi Y, Del Giudice M, et al (2023)

Working from anywhere: yin-yang cognition paradoxes of knowledge sharing and hiding for developing careers in China.

Humanities & social sciences communications, 10(1):239.

Digital technology coupled with the quarantines caused by the COVID-19 pandemic has made working from anywhere (WFA)-a modern form of remote working-a widespread phenomenon. Given that WFA brings new career challenges to and engenders paradoxes of knowledge exchange among employees, this research aims to examine how the interactions of remote work time (RWT), knowledge sharing (KS), and knowledge hiding (KH) affect career development (CD) from a culturally grounded paradoxical framing of yin-yang harmonizing. The data were collected from Chinese manufacturing employees, and a moderated hierarchical regression analysis was used to examine the hypotheses. The results show an inverted U-shaped relationship between RWT and CD. The interaction of KS and KH is significantly related to CD, and the inverted U-shaped RWT-CD relationship is moderated by the interaction term, in which RWT exerts the most substantial positive impact on CD when KS is high and KH is low. This study offers valuable implications for coping with perplexing employment relationships and increasing career challenges in volatile work environments. The primary originality is to adopt a novel cognitive frame of yin-yang harmonizing to examine the nonlinear effect of remote working and the symbiotic impact of KS and KH on CD, which not only enriches the understanding of flexible work arrangements in the digital economy but also provides novel insights into the interconnectedness of KS and KH and their interacting effects on HRM-related outcomes.

RevDate: 2023-05-22

Babaie E, Hassanpour K, Aldaghi M, et al (2023)

Comparison of the effect of ursodeoxycholic acid and multistrain synbiotic on indirect hyperbilirubinemia among neonates treated with phototherapy: A double-blind, randomized, placebo-controlled clinical trial study.

Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences, 28:40.

BACKGROUND: This study was aimed at evaluating the effect of ursodeoxycholic acid (UDCA) and multistrain synbiotic on indirect hyperbilirubinemia among neonates treated with phototherapy.

MATERIALS AND METHODS: This double-blind, randomized clinical trial was conducted on 120 subjects presenting with indirect hyperbilirubinemia in 2019. Subjects were randomly divided into three groups of synbiotic, UDCA, and control. The synbiotic group received five drops/day of synbiotic in addition to phototherapy. UDCA group received 10 mg/kg/day of Ursobil divided every 12 h in addition to phototherapy. The Control group received a placebo (water) in addition to phototherapy. Phototherapy was discontinued when the bilirubin levels reached <10 mg/dL. Total bilirubin levels were measured using the diazo method at 12, 24, and 36 h after hospitalization. This study used repeated measure analysis of variance and post hoc tests.

RESULTS: The mean total of bilirubin was substantially decreased in both synbiotic and UDCA groups as compared to the control group at 24 h after hospitalization (P < 0.001). Moreover, the Bonferroni post hoc test showed significant differences regarding the mean total of bilirubin between the three groups (P < 0.05) except for the association between UDCA and synbiotic at 24 h after hospitalization (P > 0.99).

CONCLUSION: Findings suggest that UDCA and synbiotic administration alongside phototherapy are more effective in reducing bilirubin levels as compared to phototherapy alone.

RevDate: 2023-05-22

Salar S, Ball NE, Baaziz H, et al (2023)

The structural analysis of the periplasmic domain of Sinorhizobium meliloti chemoreceptor McpZ reveals a novel fold and suggests a complex mechanism of transmembrane signaling.

Proteins [Epub ahead of print].

Chemotaxis is a fundamental process whereby bacteria seek out nutrient sources and avoid harmful chemicals. For the symbiotic soil bacterium Sinorhizobium meliloti, the chemotaxis system also plays an essential role in the interaction with its legume host. The chemotactic signaling cascade is initiated through interactions of an attractant or repellent compound with chemoreceptors or methyl-accepting chemotaxis proteins (MCPs). S. meliloti possesses eight chemoreceptors to mediate chemotaxis. Six of these receptors are transmembrane proteins with periplasmic ligand-binding domains (LBDs). The specific functions of McpW and McpZ are still unknown. Here, we report the crystal structure of the periplasmic domain of McpZ (McpZPD) at 2.7 Å resolution. McpZPD assumes a novel fold consisting of three concatenated four-helix bundle modules. Through phylogenetic analyses, we discovered that this helical tri-modular domain fold arose within the Rhizobiaceae family and is still evolving rapidly. The structure, offering a rare view of a ligand-free dimeric MCP-LBD, reveals a novel dimerization interface. Molecular dynamics calculations suggest ligand binding will induce conformational changes that result in large horizontal helix movements within the membrane-proximal domains of the McpZPD dimer that are accompanied by a 5 Å vertical shift of the terminal helix toward the inner cell membrane. These results suggest a mechanism of transmembrane signaling for this family of MCPs that entails both piston-type and scissoring movements. The predicted movements terminate in a conformation that closely mirrors those observed in related ligand-bound MCP-LBDs.

RevDate: 2023-05-22

Sisti LS, Pena-Passos M, J Lishcka Sampaio Mayer (2023)

Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants.

Journal of visualized experiments : JoVE.

Mycoheterotrophic plants present one of the most extreme forms of mycorrhizal dependency, having totally lost their autotrophic capacity. As essential as any other vital resource, the fungi with which these plants intimately associate are essential for them. Hence, some of the most relevant techniques in studying mycoheterotrophic species are the ones that enable the investigation of associated fungi, especially those inhabiting roots and subterranean organs. In this context, techniques for identifying culture-dependent and culture-independent endophytic fungi are commonly applied. Isolating fungal endophytes provides a means for morphologically identifying them, analyzing their diversity, and maintaining inocula for applications in the symbiotic germination of orchid seeds. However, it is known that there is a large variety of non-culturable fungi inhabiting plant tissues. Thus, culture-independent molecular identification techniques offer a broader cover of species diversity and abundance. This article aims to provide the methodological support necessary for starting two investigation procedures: a culture-dependent and an independent one. Regarding the culture-dependent protocol, the processes of collecting and maintaining plant samples from collection sites to laboratory facilities are detailed, along with isolating filamentous fungi from subterranean and aerial organs of mycoheterotrophic plants, keeping a collection of isolates, morphologically characterizing hyphae by slide culture methodology, and molecular identification of fungi by total DNA extraction. Encompassing culture-independent methodologies, the detailed procedures include collecting plant samples for metagenomic analyses and total DNA extraction from achlorophyllous plant organs using a commercial kit. Finally, continuity protocols (e.g., polymerase chain reaction [PCR], sequencing) are also suggested for analyses, and techniques are presented here.

RevDate: 2023-05-22

Lin J, Wi D, Ly M, et al (2023)

Soybean Hairy Root Transformation for the Analysis of Gene Function.

Journal of visualized experiments : JoVE.

Soybean (Glycine max) is a valuable crop in agriculture that has thousands of industrial uses. Soybean roots are the primary site of interaction with soil-borne microbes that form symbiosis to fix nitrogen and pathogens, which makes research involving soybean root genetics of prime importance to improve its agricultural production. The genetic transformation of soybean hairy roots (HRs) is mediated by the Agrobacterium rhizogenes strain NCPPB2659 (K599) and is an efficient tool for studying gene function in soybean roots, taking only 2 months from start to finish. Here, we provide a detailed protocol that outlines the method for overexpressing and silencing a gene of interest in soybean HRs. This methodology includes soybean seed sterilization, infection of cotyledons with K599, and the selection and harvesting of genetically transformed HRs for RNA isolation and, if warranted, metabolite analyses. The throughput of the approach is sufficient to simultaneously study several genes or networks and could determine the optimal engineering strategies prior to committing to long-term stable transformation approaches.

RevDate: 2023-05-22

Robbins C, Cruz Corella J, Aletti C, et al (2023)

Generation of disproportionate nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription.

RevDate: 2023-05-21

Hnini M, El Attar I, Taha K, et al (2023)

Genetic diversity, symbiotic efficiency, stress tolerance, and plant growth promotion traits of rhizobia nodulating Vachellia tortilis subsp. raddiana growing in dryland soils in southern Morocco.

Systematic and applied microbiology, 46(4):126434 pii:S0723-2020(23)00043-7 [Epub ahead of print].

In the present study, we analyzed the genetic diversity, phylogenetic relationships, stress tolerance, phytobeneficial traits, and symbiotic characteristics of rhizobial strains isolated from root nodules of Vachellia tortilis subsp. raddiana grown in soils collected in the extreme Southwest of the Anti-Atlas Mountains in Morocco. Subsequent to Rep-PCR fingerprinting, 16S rDNA gene sequencing of 15 representative strains showed that all of them belong to the genus Ensifer. Phylogenetic analysis and concatenation of the housekeeping genes gyrB, rpoB, recA, and dnaK revealed that the entire collection (except strain LMR678) shared 99.08 % to 99.92% similarity with Ensifer sp. USDA 257 and 96.92% to 98.79% with Sinorhizobium BJ1. Phylogenetic analysis of nodC and nodA sequences showed that all strains but one (LMR678) formed a phylogenetic group with the type strain "E. aridi" LMR001[T] (similarity over 98%). Moreover, it was relevant that most strains belong to the symbiovar vachelliae. In vitro tests revealed that five strains produced IAA, four solubilized inorganic phosphate, and one produced siderophores. All strains showed tolerance to NaCl concentrations ranging from 2 to 12% and grew at up to 10% of PEG6000. A greenhouse plant inoculation test conducted during five months demonstrated that most rhizobial strains were infective and efficient. Strains LMR688, LMR692, and LMR687 exhibited high relative symbiotic efficiency values (respectively 231.6 %, 171.96 %, and 140.84 %). These strains could be considered as the most suitable candidates for inoculation of V. t. subsp. raddiana, to be used as a pioneer plant for restoring arid soils threatened with desertification.

RevDate: 2023-05-20

Lang H, Wang H, Wang H, et al (2023)

Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees.

Nature communications, 14(1):2778.

Nosema ceranae is an intracellular parasite invading the midgut of honeybees, which causes serious nosemosis implicated in honeybee colony losses worldwide. The core gut microbiota is involved in protecting against parasitism, and the genetically engineering of the native gut symbionts provides a novel and efficient way to fight pathogens. Here, using laboratory-generated bees mono-associated with gut members, we find that Snodgrassella alvi inhibit microsporidia proliferation, potentially via the stimulation of host oxidant-mediated immune response. Accordingly, N. ceranae employs the thioredoxin and glutathione systems to defend against oxidative stress and maintain a balanced redox equilibrium, which is essential for the infection process. We knock down the gene expression using nanoparticle-mediated RNA interference, which targets the γ-glutamyl-cysteine synthetase and thioredoxin reductase genes of microsporidia. It significantly reduces the spore load, confirming the importance of the antioxidant mechanism for the intracellular invasion of the N. ceranae parasite. Finally, we genetically modify the symbiotic S. alvi to deliver dsRNA corresponding to the genes involved in the redox system of the microsporidia. The engineered S. alvi induces RNA interference and represses parasite gene expression, thereby inhibits the parasitism significantly. Specifically, N. ceranae is most suppressed by the recombinant strain corresponding to the glutathione synthetase or by a mixture of bacteria expressing variable dsRNA. Our findings extend our previous understanding of the protection of gut symbionts against N. ceranae and provide a symbiont-mediated RNAi system for inhibiting microsporidia infection in honeybees.

RevDate: 2023-05-20

Sun H, Xie Z, Yang X, et al (2023)

New insights into microbial and metabolite signatures of coral bleaching.

The Science of the total environment pii:S0048-9697(23)02879-6 [Epub ahead of print].

Coral bleaching and coral reef degradation have been severely increased due to anthropogenic impacts, especially global warming. Studies have indicated the key role of host-microbiome symbiotic relationships for the coral holobiont health and development, although not all of the mechanisms of interaction have been fully explored. Here, we explore bacterial and metabolic shifts within coral holobionts under thermal stress, and its correlation with bleaching. Our results showed obvious signs of coral bleaching after 13 days of heating treatment, and a more-complex co-occurrence network was observed in the coral-associated bacterial community of the heating group. The bacterial community and metabolites changed significantly under thermal stress, and genera Flavobacterium, Shewanella and Psychrobacter increased from <0.1 % to 43.58 %, 6.95 % and 6.35 %, respectively. Bacteria potentially associated with stress tolerance, biofilm formation and mobile elements decreased from 80.93 %, 62.15 % and 49.27 % to 56.28 %, 28.41 % and 18.76 %, respectively. The differentially expressed metabolites of corals after heating treatment, such as Cer(d18:0/17:0), 1-Methyladenosine, Trp-P-1 and Marasmal, were associated with cell cycle regulation and antioxidant properties. Our results can contribute to our current understanding on the correlations between coral-symbiotic bacteria, metabolites and the coral physiological response to thermal stress. These new insights into the metabolomics of heat-stressed coral holobionts may expand our knowledge on the mechanisms underlying bleaching.

RevDate: 2023-05-20

Chen X, Hu X, Wang H, et al (2023)

GmBES1-1 dampens the activity of GmNSP1/2 to mediate brassinosteroid inhibition of nodulation in soybean.

Plant communications pii:S2590-3462(23)00144-X [Epub ahead of print].

Soybean (Glycine max) forms root nodule to house rhizobial bacteria for biological nitrogen fixation. The development of root nodules is intricately regulated by endogenous and exogenous cues. The phytohormone Brassinosteroids (BRs) have been shown to negatively regulate nodulation in soybean, but the underlying genetic and molecular mechanisms remain largely unknown. Here, we performed transcriptomic analyses and revealed that BR signaling negatively regulates nodulation factor (NF) signaling. We found that BR signaling inhibits nodulation through its signaling component GmBES1-1, by dampening NF signaling and nodule formation. In addition, GmBES1-1 could directly interact with both GmNSP1 and GmNSP2 to inhibit their interaction and the DNA-binding activity of GmNSP1. Furthermore, BR-induced the nuclear accumulation of GmBES1-1 is essential for inhibiting nodulation. Taken together, the regulation of the subcellular localization of GmBES1-1 by BRs plays a key role in legume-rhizobium symbiosis and plant development, which reports a crosstalk mechanism between phytohormonal and symbiotic signaling pathways.

RevDate: 2023-05-19

Karaseva NP, Rimskaya-Korsakova NN, Kokarev VN, et al (2023)

Distribution of Siboglinids (Annelida, Siboglinidae) in the Laptev Sea and Adjacent Areas of the Arctic Basin.

Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections, 509(1):124-127.

Biodiversity in the Laptev Sea was assessed for gutless marine worms of the family Siboglinidae (Annelida), whose metabolism is provided by symbiotic bacteria that oxidize hydrogen sulfide and methane. Seven siboglinid species were found within the geographical boundaries of the Laptev Sea, and another species was found in an adjacent sector of the Arctic Basin. The largest number of finds and the greatest biological diversity of siboglinids were observed in the eastern part of the Laptev Sea in a field of numerous methane flares. One find was made in the estuary area of the Lena River at a depth of 25 m. A possible association of siboglinids with methane seepage areas is discussed.


RJR Experience and Expertise


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.


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.


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.


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.


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.


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.


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.


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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