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The gut microbiota plays an essential role in its host's nutrition, development and behavior. Although crickets are becoming major ecosystemic model systems and have important societal applications, such as alternative animal proteins or biocatalysts, little is known about their gut microbiome acquisition and how environmental factors shape this community. Therefore, in this study, we exposed sand field crickets to soils with different characteristics and microbial communities to test the influence of these on gut microbial community composition. We used 16S/18S rRNA gene Illumina sequencing to analyze different soil and gut communities, targeting the three domains of life, Archaea, Bacteria, and Eukaryotes. Our results showed a dominance of Mucoromycota fungi and Bacteroidota in the gut microbiota. We were unable to retrieve sufficient read numbers for the Archaea. Most of the microbial taxa that were identified can degrade soil-derived complex organic matter, likely helping the host digest its food. The soil characteristics had a significant impact on the gut microbial community structure, supporting our assumption that the environment plays an essential role in gut microbiota acquisition. Host sex also had an impact on the gut community, possibly because the female guts were bigger in mass, leading to differences in oxygen concentrations. [ABSTRACT FROM AUTHOR]

Terrestrial subsurface microbial communities are not restricted to the fluid-filled void system commonly targeted during groundwater sampling but are able to inhabit and dwell in rocks. However, compared to the exploration of the deep biosphere, endolithic niches in shallow sedimentary bedrock have received little interest so far. Despite the potential contribution of rock matrix dwellers to matter cycling and groundwater resource quality, their identity and diversity patterns are largely unknown. Here, we investigated the bacterial diversity in twenty-two rock cores in common limestone-mudstone alternations that differed in rock permeabilities and other geostructural and petrological factors. 16S rRNA gene analysis showed the existence of a unique rock matrix microbiome compared to surrounding groundwater. Typically, shallow weathered limestones contained bacterial groups most likely originating from soil habitats. In low-permeable mudstones, we found similar communities of oligotrophic heterotrophs, and thiosulfate-oxidizing autotrophs, without relation to depth, rock type and bulk rock permeability. In fractured limestone, the bacterial communities of fracture surfaces were distinct from their matrix counterparts and ranged from organic matter decomposers in outcrop areas to autotrophs in downdip positions that receive limited surface input. Contrastingly, rock matrices from lithologically corresponding, but highly isolated environments, were dominated by spore-forming bacteria, oligotrophic heterotrophs and hydrogen-oxidizing autotrophs. Neither depth, matrix permeability nor major mineralogy dominantly controlled the endolithic bacterial diversity. Instead, a combination of subsurface factors drives the supply of niches by fluids, matter and energy as well as the (re)dispersal conditions that likely shape bacterial diversity. Unlabelled Image • Bacterial patterns differ between niches of high- and low-bulk rock permeability • Depth and matrix permeability are minor controls of endolithic diversity. • Surface input or isolation control endolithic bacterial communities • Oligotrophic heterotrophs dominate bacterial communities in isolated niches • Bacterial communities on fracture surfaces differ from those inside the matrices. [ABSTRACT FROM AUTHOR]

Investigations of the biogeochemical roles of benthic A rchaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group ( MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-C oA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment. [ABSTRACT FROM AUTHOR]

Sediments of the White Oak River ( WOR) estuary are situated on the coast of North Carolina harbour, one of the most diverse known populations of uncultured Archaea, specifically the miscellaneous Crenarchaeotal group ( MCG). In order to constrain the environmental factors influencing the uncultured archaeal groups in the WOR estuary, biogeochemical profiles as well as archaeal 16 S rRNA genes from sediment pushcores were analysed. The relative fraction of MCG A rchaea in clone libraries decreased at shallow sediment depths (27% of the total MCG). A LINKTREE analysis of the MCG intragroup diversity reinforced the observation that the MCG subgroup 6 was found predominantly within sulfide-depleted shallow sediment layers; other subgroups (especially MCG-1 and MCG-5/8) occurred preferentially in deeper, more strongly reducing sediment layers. The available evidence from this study and published MCG distribution patterns indicates that the MCG-6 subgroup is a specialized MCG lineage that, in contrast to other MCG subgroups, prefers suboxic sediment horizons with minimal or no free sulfide. Collectively, our results reveal the habitat preferences of different MCG subgroups in the WOR sediments and suggest that physiological adaptations to distinct sedimentary geochemical niches evolved in different MCG subgroups. [ABSTRACT FROM AUTHOR]

The introduction of NaCl in freshwater caused by winter runoffs is a problem whose consequences are still little understood. We sought to analyze the effect of NaCl addition on microbial communities of the hypolimnion and bottom sediments of a Canadian lake. Using microcosms comprising a salinity gradient varying between 0.01 and 3.22 ppt (10–3220 mg/L−1) NaCl, we investigated the effect of salinity on prokaryotic absolute abundance and diversity, following a three- and six-week exposure, and detected the presence of a salinity threshold for microbial communities' differentiation. We observed a significant decline of bacterial diversity after six weeks in hypolimnetic samples. In the sediments, no clear effect of NaCl was observed on abundance or diversity, despite the presence of variations throughout the salinity gradient. The implication of nutrient fluctuations as well as the co-occurrence of species and inter-domain interactions is likely and would strongly contribute to the development of salt-exposed prokaryotic communities. In hypolimnetic water and sediments, the archaeal and eukaryotic communities differed significantly from 0.93 ppt (930 mg/L−1), while only conclusive at 1.9 ppt (1900 mg/L−1) NaCl in bacteria, meaning that the regulations in place are possibly suitable for the protection of the microbial communities in the hypolimnion and sediment lake layers. [ABSTRACT FROM AUTHOR]

Highlights: [•] Ethylene, ethanethiol and propanethiol stimulated production of the alkane. [•] Ethylene as substrate that gave the highest yield of alkane. [•] Methanogens were suggested to be involved in generation of the alkane. [•] H2 partial pressure required to stimulate ethanogenesis from ethylene was <0.01% H2. [•] Methanocalculus is a possible candidate for ethanogenesis from ethylene. [Copyright &y& Elsevier]

Marine mud volcanoes are geological structures emitting large amounts of methane from their active centres. The Amsterdam mud volcano ( AMV), located in the Anaximander Mountains south of Turkey, is characterized by intense active methane seepage produced in part by methanogens. To date, information about the diversity or the metabolic pathways used by the methanogens in active centres of marine mud volcanoes is limited. 14 C-radiotracer measurements showed that methylamines/methanol, H2/ CO2 and acetate were used for methanogenesis in the AMV. Methylotrophic methanogenesis was measured all along the sediment core, Methanosarcinales affiliated sequences were detected using archaeal 16 S PCR- DGGE and mcrA gene libraries, and enrichments of methanogens showed the presence of Methanococcoides in the shallow sediment layers. Overall acetoclastic methanogenesis was higher than hydrogenotrophic methanogenesis, which is unusual for cold seep sediments. Interestingly, acetate porewater concentrations were extremely high in the AMV sediments. This might be the result of organic matter cracking in deeper hotter sediment layers. Methane was also produced from hexadecanes. For the most part, the methanogenic community diversity was in accordance with the depth distribution of the H2/ CO2 and acetate methanogenesis. These results demonstrate the importance of methanogenic communities in the centres of marine mud volcanoes. [ABSTRACT FROM AUTHOR]

Summary Submarine mud volcanoes are a significant source of methane to the atmosphere. The Napoli mud volcano, situated in the brine-impacted Olimpi Area of the Eastern Mediterranean Sea, emits mainly biogenic methane particularly at the centre of the mud volcano. Temperature gradients support the suggestion that Napoli is a cold mud volcano with moderate fluid flow rates. Biogeochemical and molecular genetic analyses were carried out to assess the methanogenic activity rates, pathways and diversity in the hypersaline sediments of the centre of the Napoli mud volcano. Methylotrophic methanogenesis was the only significant methanogenic pathway in the shallow sediments (0-40 cm) but was also measured throughout the sediment core, confirming that methylotrophic methanogens could be well adapted to hypersaline environments. Hydrogenotrophic methanogenesis was the dominant pathway below 50 cm; however, low rates of acetoclastic methanogenesis were also present, even in sediment layers with the highest salinity, showing that these methanogens can thrive in this extreme environment. PCR-DGGE and methyl coenzyme M reductase gene libraries detected sequences affiliated with anaerobic methanotrophs (mainly ANME-1) as well as Methanococcoides methanogens. Results show that the hypersaline conditions in the centre of the Napoli mud volcano influence active biogenic methane fluxes and methanogenic/methylotrophic diversity. [ABSTRACT FROM AUTHOR]

Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano. [ABSTRACT FROM AUTHOR]

Siboglinid tubeworms in cold seep sediments can locally modify the geochemical gradients of electron acceptors and donors, hence creating potential microhabitats for prokaryotic populations. The archaeal communities associated with sediments populated by Oligobrachia haakonmosbiensis and Sclerolinum contortum Siboglinid tubeworms in the Storegga Slide were examined in this study. Vertical distribution of archaeal communities was investigated using denaturing gradient gel electrophoresis based on 16S rRNA genes. The active fraction of the archaeal community was assessed by using reverse-transcribed rRNA. Archaeal communities associated with sediments colonized by tubeworms were affiliated with uncultivated archaeal lineages of the Crenarchaeota and Euryarchaeota. The composition of the active archaeal populations changed with depth indicating a reorganization of microbial communities. 16S rRNA gene libraries were dominated by sequences affiliated to the Rice Cluster V which are unusual in marine sediment samples. Moreover, this study provides the first evidence of living Crenarchaeota of the Rice Cluster V in cold seep sediments. Furthermore, the Storegga Slide sediments harbored a high diversity of other minor groups of uncultivated lineages including Terrestrial Miscellaneous Euryarchaeotal Group, Marine Benthic Group (MBG)-D, MBG-E, Deep-Sea Hydrothermal Vent Euryarchaeotal Group, Lake Dagow Sediment, Val Kotinen Lake clade III, and Sippenauer Moor 1. Thus, we hypothesize that the vertical geochemical imprint created by the tubeworms could support broad active archaeal populations in the Siboglinidae-populated Storegga Slide sediments. [ABSTRACT FROM AUTHOR]

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes. [ABSTRACT FROM AUTHOR]

Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km2 in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities. [ABSTRACT FROM AUTHOR]

Aquifers are rich in microbial diversity. However, there is a lack of information about sessile communities in these environments because of the difficulty in sampling fresh in situ rock surfaces. Thus, this study's objective was to better understand the sessile community in a fractured aquifer. Additionally, the impact of the rock mineral composition on microbial community composition during colonization was explored. Using a system of bioreactors, we recreated the environmental conditions of a 1.5 m deep aquifer in Covey Hill (QC, Canada) using groundwater samples collected from the site. We carried out 16S/18S rRNA amplicon sequencing of the water and sessile communities after 24 days of incubation. Our data showed that many microbial taxa overlapped between the sessile and planktonic communities, indicating colonization of the solid surfaces. Quartz and feldspar had a significant impact on bacterial community structure. Sessile communities were dominated by Gaillonella, Alkanindiges, unclassified Acetobacteraceae, Apoikiales, Glissomonadida, and Synurales. We could not detect any Archaea in the sessile community. The sessile communities contained bacterial genera involved in iron cycling and adapted to acidic and low-carbon-concentration environments. Eukaryotic predators dominated the sessile community. [ABSTRACT FROM AUTHOR]

The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts. [ABSTRACT FROM AUTHOR]

Abandoned and flooded ore mines are examples of hostile environments (cold, dark, oligotrophic, trace metal) with a potential vast diversity of microbial communities rarely characterized. This study aimed to understand the effects of depth, the source of water (surface or groundwater), and abiotic factors on the communities present in the old Forsyth iron mine in Quebec (Canada). Water and biofilm samples from the mine were sampled by a team of technical divers who followed a depth gradient (0 to 183 m deep) to study the planktonic and sessile communities' diversity and structure. We used 16S/18S rRNA amplicon to characterize the taxonomic diversity of Bacteria, Archaea, and Eukaryotes. Our results show that depth was not a significant factor explaining the difference in community composition observed, but lifestyle (planktonic/sessile) was. We discovered a vast diversity of microbial taxa, with taxa involved in carbon- and sulfur-cycling. Sessile communities seem to be centered on C1-cycling with fungi and heterotrophs likely adapted to heavy-metal stress. Planktonic communities were dominated by ultra-small archaeal and bacterial taxa, highlighting harsh conditions in the mine waters. Microbial source tracking indicated sources of communities from surface to deeper layers and vice versa, suggesting the dispersion of organisms in the mine, although water connectivity remains unknown. [ABSTRACT FROM AUTHOR]

The fish gut microbiome plays an essential role in the host's development and survival. Environmental factors can shape the gut microbiome and potentially mediate physiological performance. Seasonal environments that experience regular abiotic and biotic transitions likely drive variability in the gut microbiome. However, we know very little about how seasonal transitions interact with the gut microbiome, especially at northern latitudes where seasonality is exaggerated. Therefore, in this study, we analyzed the native gut microbiome of a flexible top predator fish species, the lake trout, across seasons in a boreal lake using 16S rRNA sequencing. Seasonal changes explained one third of the bacterial variance. The relative abundance of several bacterial taxa influenced the observed seasonal differences in the community; pathogenic Pseudomonas and Stenotrophomonas were most abundant in the spring and winter seasons, and chemoheterotrophic Macrococcus and Lelliottia were most abundant in the summer. The fall season was dominated by unclassified Clostridiaceae, potentially linked to a shift in lake trout foraging. Therefore, we present novel evidence that suggests seasonality is likely to shape the native gut microbiome of lake trout; however, the mechanistic links between the environment and the microbial diversity of the gut remain to be uncovered. [ABSTRACT FROM AUTHOR]

We investigated the microbial community compositions in two sediment samples from the acidic ( pH ∼3) and hypersaline (>4.5% NaCl) surface waters, which are widespread in Western Australia. In West Dalyup River, large amounts of NaCl, Fe( II) and sulfate are brought by the groundwater into the surface run-off. The presence of K-jarosite and schwertmannite minerals in the river sediments suggested the occurrence of microbial Fe( II) oxidation because chemical oxidation is greatly reduced at low pH. 16S r RNA gene diversity analyses revealed that sequences affiliated with an uncultured archaeal lineage named Aplasma, which has the genomic potential for Fe( II) oxidation, were dominant in both sediment samples. The acidophilic heterotrophs A cidiphilium and A cidocella were identified as the dominant bacterial groups. A cidiphilium strain AusYE3-1 obtained from the river sediment tolerated up to 6% NaCl at pH 3 under oxic conditions and cells of strain AusYE3-1 reduced the effects of high salt content by forming filamentous structure clumping as aggregates. Neither growth nor Fe( III) reduction by strain AusYE3-1 was observed in anoxic salt-containing medium. The detection of Aplasma group as potential Fe( II) oxidizers and the inhibited Fe( III)-reducing capacity of A cidiphilium contributes to our understanding of the microbial ecology of acidic hypersaline environments. [ABSTRACT FROM AUTHOR]

In freshwater ecosystems, dynamic hydraulic events (floods or dam maintenance) lead to sediment resuspension and mixing with waters of different composition. Microbial communities living in the sediments play a major role in these leaching events, contributing to organic matter degradation and the release of trace elements. However, the dynamics of community diversity are seldom studied in the context of ecological studies. Therefore, we carried out laboratory-induced leaching experiments, using sediments from the Villerest dam reservoir (Villerest, France). To assess whole microbial community diversity, we sequenced the archaeal and bacterial 16S rRNA genes using Illumina MiSeq. Our results suggest that the degree of dissolved oxygen found in the water during these resuspension episodes influenced community dynamics, with anoxic waters leading to drastic shifts in sedimentary communities compared to oxic waters. Furthermore, the release of microbial cells from sediments to the water column were more favorable to water colonization when events were caused by oxic waters. Most of the bacteria found in the sediments were chemoorganotrophs and most of the archaea were methanogens. Methylotrophic, as well as archaeal, and bacterial chemoorganotrophs were detected in the leachate samples. These results also show that organic matter degradation occurred, likely participating in carbonate dissolution and the release of trace elements during freshwater resuspension events. [ABSTRACT FROM AUTHOR]

Each year, millions of tons of sodium chloride are dumped on roads, contributing to the salinization of freshwater environments. Thus, we sought to understand the effect of sodium chloride (NaCl) on freshwater lake prokaryotic communities, an important and understudied component of food webs. Using mesocosms with 0.01–2.74 ppt NaCl (0.27–1110.86 mg/L Cl−), we evaluated the effect generated on the diversity and absolute abundance of prokaryotic populations after three and six weeks. A positive relationship between Cl− values and absolute bacterial abundance was found after three weeks. The influence of eukaryotic diversity variation was observed as well. Significant differentiation of bacterial communities starting at 420 mg/L Cl− was observed after three weeks, levels lower than the Canadian and US recommendations for acute chloride exposure. The partial recovery of a "pre-disturbance" community was observed following a drop in salinity at the threshold level of 420 mg/L Cl−. A gradual transition of dominance from Betaproteobacteria and Actinobacteria to Bacteroidia and Alphaproteobacteria was observed and is overall similar to the natural transition observed in estuaries. [ABSTRACT FROM AUTHOR]