Microbial Lineages Research Articles

Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea

Abstract. There is a growing recognition of the role of particle-attached (PA) and free-living (FL) microorganisms in marine carbon cycle. However, current understanding of PA and FL microbial communities is largely focused on those in the upper photic zone, and relatively fewer studies have focused on microbial communities of the deep ocean. Moreover, archaeal populations receive even less attention. In this study, we determined bacterial and archaeal community structures of both the PA and FL assemblages at different depths, from the surface to the bathypelagic zone along two water column profiles in the South China Sea. Our results suggest that environmental parameters including depth, seawater age, salinity, particulate organic carbon (POC), dissolved organic carbon (DOC), dissolved oxygen (DO) and silicate play a role in structuring these microbial communities. Generally, the PA microbial communities had relatively low abundance and diversity compared with the FL microbial communities at most depths. Further microbial community analysis revealed that PA and FL fractions generally accommodate significantly divergent microbial compositions at each depth. The PA bacterial communities mainly comprise members of Alphaproteobacteria and Gammaproteobacteria, together with some from Planctomycetes and Deltaproteobacteria, while the FL bacterial lineages are also mostly distributed within Alphaproteobacteria and Gammaproteobacteria, along with other abundant members chiefly from Actinobacteria, Cyanobacteria, Bacteroidetes, Marinimicrobia and Deltaproteobacteria. Moreover, there was an obvious shifting in the dominant PA and FL bacterial compositions along the depth profiles from the surface to the bathypelagic deep. By contrast, both PA and FL archaeal communities dominantly consisted of euryarchaeotal Marine Group II (MGII) and thaumarchaeotal Nitrosopumilales, together with variable amounts of Marine Group III (MGIII), Methanosarcinales, Marine Benthic Group A (MBG-A) and Woesearchaeota. However, the pronounced distinction of archaeal community compositions between PA and FL fractions was observed at a finer taxonomic level. A high proportion of overlap of microbial compositions between PA and FL fractions implies that most microorganisms are potentially generalists with PA and FL dual lifestyles for versatile metabolic flexibility. In addition, microbial distribution along the depth profile indicates a potential vertical connectivity between the surface-specific microbial lineages and those in the deep ocean, likely through microbial attachment to sinking particles.

Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert.

Understanding microbial niche variability in polar regions can provide insights into the adaptive diversification of microbial lineages in extreme environments. Compositions of microbial communities in Arctic soils are well documented but a comprehensive multidomain diversity assessment of rocks remains insufficiently studied. In this study, we obtained two types of rocks (sandstone and limestone) and soils around the rocks in a high Arctic polar desert (Svalbard), and examined the compositions of archaeal, bacterial, fungal, and protistan communities in the rocks and soils. The microbial community structure differed significantly between rocks and soils across all microbial groups at higher taxonomic levels, indicating that Acidobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, Leotiomycetes, Pezizomycetes, Mortierellomycetes, Sarcomonadea, and Spirotrichea were more abundant in soils, whereas Cyanobacteria, Deinococcus-Thermus, FBP, Lecanoromycetes, Eurotiomycetes, Trebouxiophyceae, and Ulvophyceae were more abundant in rocks. Interestingly, fungal communities differed markedly between two different rock types, which is likely to be ascribed to the predominance of distinct lichen-forming fungal taxa (Verrucariales in limestone, and Lecanorales in sandstone). This suggests that the physical or chemical properties of rocks could be a major determinant in the successful establishment of lichens in lithic environments. Furthermore, the biotic interactions among microorganisms based on co-occurrence network analysis revealed that Polyblastia and Verrucaria in limestone, and Atla, Porpidia, and Candelariella in sandstone play an important role as keystone taxa in the lithic communities. Our study shows that even in niches with the same climate regime and proximity to each other, heterogeneity of edaphic and lithic niches can affect microbial community assembly, which could be helpful in comprehensively understanding the effects of niche on microbial assembly in Arctic terrestrial ecosystems.

Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition

Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, Po concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.

Distribution and Succession of Microbial Communities Along the Dispersal Pathway of Hydrothermal Plumes on the Southwest Indian Ridge

The distribution and succession of microbial communities along the dispersion path of hydrothermal plumes has not been well investigated. In this study, we collected several types of samples from the Longqi hydrothermal field located on the Southwest Indian Ridge, including hydrothermal plumes at different stages of formation, a suite of water column samples across the non-buoyant hydrothermal plumes above this field, and a background seawater column approximately 350 km away from the hydrothermal field. Using CH4 concentration anomalies, three non-buoyant plume samples between 2,535 m and 2,735 m were identified within the water column. Microbial community compositions within these plumes and background seawater samples were examined based on the 16S rRNA genes and revealed significant variations and successions in community composition between different portions of the hydrothermal plumes. Near the vent orifice, representing the initial stage of plume formation, microbial populations were characterized by abundant and diverse putative vent-associated communities including (hyper)thermophiles such as Aquificaceae and Hydrogenothermaceae within the phylum Aquificae, and some epsilonproteobacterial chemolithoautotrophs such as Sulfurovum, Sulfurimonas, and Caminibacter. By contrast, in the rising buoyant plumes and adjacent seawaters, most vent-associated microbial taxa were still present but made only minor contributions to community composition. Some microbial taxa that are common in seawater columns such as alphaproteobacterial Sphingomonadaceae and SAR11 clade, deltaproteobacterial SAR324 clade, and gammaproteobacterial Pseudomonas, together with Sulfurimonas and SUP05 clade, became predominant. Members within the Sulfurimonas and SUP05 clade flourished with considerable abundance in the non-buoyant plumes, although these plumes were mainly composed of alphaproteobacterial Rhodobacteraceae, gammaproteobacterial Alteromonadaceae and Saccharospirillaceae putatively derived from the surrounding ambient seawater. We also analyzed archaeal components in the initial discharge and rising buoyant plume stages, with both primarily consisting of thaumarchaeal Nitrosopumilales and euryarchaeal Marine Group II. Our results indicated that being characteristic microbial lineages within the hydrothermal plumes of the Southwest Indian Ridge, both Sulfurimonas and SUP05 clade display a common and abundant distribution across the plume path. However, out of these clades, Sulfurimonas is more abundant and widespread.

NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity.

The activity of individual microorganisms can be measured within environmental samples by detecting uptake of isotope-labelled substrates using nano-scale secondary ion mass spectrometry (nanoSIMS). Recent studies have demonstrated that sample preparation can decrease 13 C and 15 N enrichment in bacterial cells, resulting in underestimates of activity. Here, we explore this effect with a variety of preparation types, microbial lineages and isotope labels to determine its consistency and therefore potential for correction. Specifically, we investigated the impact of different protocols for fixation, nucleic acid staining and catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) on >14 500 archaeal and bacterial cells (Methanosarcina acetivorans, Sulfolobus acidocaldarius and Pseudomonas putida) enriched in 13 C, 15 N, 18 O, 2 H and/or 34 S. We found these methods decrease isotope enrichments by up to 80% - much more than previously reported - and that the effect varies by taxa, growth phase, isotope label and applied protocol. We make recommendations for how to account for this effect experimentally and analytically. We also re-evaluate published nanoSIMS datasets and revise estimated microbial turnover times in the marine subsurface and nitrogen fixation rates in pelagic unicellular cyanobacteria. When sample preparation is accounted for, cell-specific rates increase and are more consistent with modelled and bulk rates.

Novel clostridial lineages recovered from metagenomes of a hot oil reservoir

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. These organisms form an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal proteins, which we propose to name UPetromonas tenebris, meaning they are single-celled organisms from dark rocks. Metagenome-assembled genomes (MAGs) of these Petromonas sp. were obtained and used to determine that these populations, while capable of spore-formation, were also likely replicating in situ in the reservoir. We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. The estimation of in-situ replication from genomic data suggest that UPetromonas tenebris lineages are functional in-situ and may be specifically adapted to inhabit oil reservoirs.

Increased litter input significantly changed the total and active microbial communities in degraded grassland soils

Increasing organic matter input and phosphorus fertilization are employed extensively to restore degraded grasslands. Nevertheless, little is known about their effects on microbes, especially on active microbial populations. Therefore, this study is aimed at examining the short-term influences of litter and phosphorus addition on microbes in degraded grassland soils. A microcosm experiment was established using soils sampled from a heavily degraded Tibetan alpine meadow. The experiment used a two-way factorial design with grass litter and phosphorus addition as the main factors. Microbial abundance and rDNA transcriptional activity were assessed through quantitative PCR. Total and active microbial community profiles were measured using DNA- and RNA-based MiSeq sequencing, respectively. As shown in this study, litter addition significantly increased microbial rDNA transcriptional activity and fungal abundance, but it decreased microbial α-diversity. However, prokaryote abundance was unaffected by the litter addition. Total and active soil microbial community profiles and interaction patterns were also significantly altered by litter addition. The relative abundance of copiotrophic and oligotrophic microbial lineages significantly increased and decreased, respectively, in the soils with litter addition. Functional predictions suggested that litter addition might significantly increase the abundance of pathogens, as well as microbes related to nitrogen fixation, denitrification, and chitinolysis, while decreasing nitrifier abundance. In contrast, no significant effects of the phosphorus addition on soil microbes were observed. These findings highlight the significant effects of increasing litter input on total and active soil microbial communities and suggest that microbial responses should be considered when restoring degraded grasslands by increasing organic matter input.

Deep Sequencing Uncovers Caste-Associated Diversity of Symbionts in the Social Ant Camponotus japonicus.

Symbiotic microorganisms can have a profound impact on the host physiology and behavior, and novel relationships between symbionts and their hosts are continually discovered. A colony of social ants consists of various castes that exhibit distinct lifestyles and is, thus, a unique model for investigating how symbionts may be involved in host eusociality. Yet our knowledge of social ant-symbiont dynamics has remained rudimentary. Through 16S rRNA gene deep sequencing of the carpenter ant Camponotus japonicus symbiont community across various castes, we here report caste-dependent diversity of commensal gut microbiota and lineage divergence of "Candidatus Blochmannia," an obligate endosymbiont. While most prevalent gut-associated bacterial populations are found across all castes (Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria), we also discovered uncultured populations that are found only in males (belonging to Corynebacteriales, Alkanindiges, and Burkholderia). Most of those populations are not detected in laboratory-maintained queens and workers, suggesting that they are facultative gut symbionts introduced via environmental acquisition. Further inspection of "Ca. Blochmannia" endosymbionts reveals that two populations are dominant in all individuals across all castes but that males preferentially contain two different sublineages that are diversified from others. Clearly, each caste has distinct symbiont communities, suggesting an overlooked biological aspect of host-symbiont interaction in social insects.IMPORTANCE Social animals, such as primates and some insects, have been shown to exchange symbiotic microbes among individuals through sharing diet or habitats, resulting in increased consistency of microbiota among social partners. The ant is a representative of social insects exhibiting various castes within a colony; queens, males, and nonreproductive females (so-called workers) show distinct morphologies, physiologies, and behaviors but tightly interact with each other in the nest. However, how this social context affects their gut microbiota has remained unclear. In this study, we deeply sequenced the gut symbiont community across various castes of the carpenter ant Camponotus japonicus We report caste-dependent diversity of commensal gut microbial community and lineage divergence of the mutualistic endosymbiont "Candidatus Blochmannia." This report sheds light on the hidden diversity in microbial populations and community structure associated with guts of males in social ants.

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

BackgroundExceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone.ResultsCo-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenome-assembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate.ConclusionsOur results indicate that excavated dinosaur bones are habitats for microorganisms including novel microbial lineages. The distinctive microhabitats and geochemistry of fossil bone interiors compared to that of the external sediment enrich a microbial biomass comprised of various novel taxa that harbor multiple gene sets related to interconnected biogeochemical processes. Therefore, the presence of these microbiomes in Mesozoic dinosaur fossils urges extra caution to be taken in the science of paleontology when hunting for endogenous biomolecules preserved from deep time.

DNA stable-isotope probing reveals potential key players for microbial decomposition and degradation of diatom-derived marine particulate matter.

Microbially mediated decomposition of particulate organic carbon (POC) is a central component of the oceanic carbon cycle, controlling the flux of organic carbon from the surface ocean to the deep ocean. Yet, the specific microbial taxa responsible for POC decomposition and degradation in the deep ocean are still unknown. To target the active microbial lineages involved in these processes, 13C‐labeled particulate organic matter (POM) was used as a substrate to incubate particle‐attached (PAM) and free‐living microbial (FLM) assemblages from the epi‐ and bathypelagic zones of the New Britain Trench (NBT). By combining DNA stable‐isotope probing and Illumina Miseq high‐throughput sequencing of bacterial 16S rRNA gene, we identified 14 active bacterial taxonomic groups that implicated in the decomposition of 13C‐labeled POM at low and high pressures under the temperature of 15°C. Our results show that both PAM and FLM were able to decompose POC and assimilate the released DOC. However, similar bacterial taxa in both the PAM and FLM assemblages were involved in POC decomposition and DOC degradation, suggesting the decoupling between microbial lifestyles and ecological functions. Microbial decomposition of POC and degradation of DOC were accomplished primarily by particle‐attached bacteria at atmospheric pressure and by free‐living bacteria at high pressures. Overall, the POC degradation rates were higher at atmospheric pressure (0.1 MPa) than at high pressures (20 and 40 MPa) under 15°C. Our results provide direct evidence linking the specific particle‐attached and free‐living bacterial lineages to decomposition and degradation of diatomic detritus at low and high pressures and identified the potential mediators of POC fluxes in the epi‐ and bathypelagic zones.

Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy.

Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.

Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution.

Plants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that nonenzymatically loosen noncovalent bonding between cellulose microfibrils. Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown. Here, we reconstruct a comprehensive phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cell wall cellulose, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi inhabit varied ecological contexts, mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present. The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Overall, expansins are unexpectedly widespread in bacteria and eukaryotes, and the contribution of these genes to microbial ecological interactions with plants and algae has probbaly been underappreciated.

Mercury geochemistry and microbial diversity in meromictic Glacier Lake, Jamesville, NY.

Meromictic lakes are stratified lakes that typically stimulate phototrophic anoxic microbial metabolism, including the transformation of sulphur. Less studied are the transformations of mercury in these environments, and the microorganisms, which mediate these reactions. In order to further an understanding of redox species, mercury and microbial populations in meromictic lakes, we examined the geochemistry and microbiology of Glacier Lake in Jamesville, NY. We found an anoxic transition at a depth of 6 m, followed by active nitrate and sulphate utilization. A chlorophyll a maximum was located at 11 m, coinciding with peaks of several photoautotrophic microbial lineages and total mercury and methyl mercury. Via amplicon sequencing, the microbial population showed pronounced peaks of cyanobacteria at 10 m, Chlorobi at 12 m and Chloroflexi at 14 m. Sulphate-reducing bacteria were also most abundant between 10 and 14 m depth. A functional gene indicating the potential for the production of methyl mercury, hgcA, was detected at several depths in the lake. Our work suggests that in addition to the sulphur cycle, the cycling of mercury may be indirectly coupled with phototrophic processes in Glacier Lake.

NanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples.

Multilocus sequence typing (MLST) is one of the most commonly used methods for studying microbial lineage worldwide. However, the traditional MLST process using Sanger sequencing is time-consuming and expensive. We have designed a workflow that simultaneously sequenced seven full-length housekeeping genes of 96 meticillin-resistant Staphylococcus aureus isolates with dual-barcode multiplexing using just a single flow cell of an Oxford Nanopore Technologies MinION system, and then we performed bioinformatic analysis for strain typing. Fifty-one of the isolates comprising 34 sequence types had been characterized using Sanger sequencing. We demonstrate that the allele assignments obtained by our nanopore workflow (nanoMLST, available at https://github.com/jade-nhri/nanoMLST) were identical to those obtained by Sanger sequencing (359/359, with 100 % agreement rate). In addition, we estimate that our multiplex system is able to perform MLST for up to 1000 samples simultaneously; thus, providing a rapid and cost-effective solution for molecular typing.

Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest.

The spatial and temporal linkages between turnover of soil microbial communities and their associated functions remain largely unexplored in terrestrial ecosystems. Yet defining these relationships and how they vary across ecosystems and microbial lineages is key to incorporating microbial communities into ecological forecasts and ecosystem models. To define linkages between turnover of soil bacterial and fungal communities and their function we sampled fungal and bacterial composition, abundance, and enzyme activities across a 3-ha area of wet tropical primary forest over 2 yr. We show that fungal and bacterial communities both exhibited temporal turnover, but turnover of both groups was much lower than in temperate ecosystems. Turnover over time was driven by gain and loss of microbial taxa and not changes in abundance of individual species present in multiple samples. Only fungi varied over space with idiosyncratic variation that did not increase linearly with distance among sampling locations. Only phosphorus-acquiring enzyme activities were linked to shifts in septate, decomposer fungal abundance; no enzymes were affected by composition or diversity of fungi or bacteria. Although temporal and spatial variation in composition was appreciable, because turnover of microbial communities did not alter the functional repertoire of decomposing enzymes, functional redundancy among taxa may be high in this ecosystem. Slow temporal turnover of tropical soil microbial communities and large functional redundancy suggests that shifts in abundance of particular functional groups may capture ecosystem function more accurately than composition in these heterogeneous ecosystems.

The Role of Land Use Types and Water Chemical Properties in Structuring the Microbiomes of a Connected Lake System.

Lakes and other freshwater bodies are intimately connected to the surrounding land, yet to what extent land-use affects the quality of freshwater and the microbial communities living in various freshwater environments is largely unknown. We address this question through an analysis of the land use surrounding 46 inter-connected lakes located within seven different drainage basins in northern Germany, and the microbiomes of these lakes during early summer. Lake microbiome structure was not correlated with the specific drainage basin or by basin size, and bacterial distribution did not seem to be limited by distance. Instead, land use within the drainage basin could predict, to some extent, NO2 + NO3 concentrations in the water, which (together with temperature, chlorophyll a and total phosphorus) correlated to some extent with the water microbiome structure. Land use directly surrounding the water bodies, however, had little observable effects on water quality or the microbiome. Several microbial lineages, including Cyanobacteria and Verrucomicrobia, were differentially partitioned between the lakes. Significantly more data, including time-series measurements of land use and water chemical properties, are needed to fully understand the interaction between the environment and the organization of microbial communities.

The Diversity and Distribution of Wolbachia, Rhizobiales, and Ophiocordyceps Within the Widespread Neotropical Turtle Ant, Cephalotes atratus (Hymenoptera: Formicidae).

Ants are an ecologically and evolutionarily diverse group, and they harbor a wide range of symbiotic microbial communities that often greatly affect their biology. Turtle ants (genus Cephalotes) engage in mutualistic relationships with gut bacteria and are exploited by microbial parasites. Studies have shown that associations among these microbial lineages and the turtle ant hosts vary geographically. However, these studies have been limited, and thorough within-species analyses of the variation and structure of these microbial communities have yet to be conducted. The giant turtle ant, Cephalotes atratus (Linnaeus 1758), is a geographically widespread, genetically diverse Neotropical species that has been sampled extensively across its geographic range, making it ideal for analysis of microbial associations. In this study, we verified the presence, genetic variation, and geographic patterns at the individual, colony, and population level of three microbial groups associated with the giant turtle ant: Wolbachia, a genus of facultative bacteria which are often parasitic, affecting host reproduction; Rhizobiales, a mutualistic order of bacteria hypothesized to be an obligate nutritional symbiont in turtle ants; and Ophiocordyceps, a genus of endoparasitic fungi infecting many arthropod species by manipulating their behavior for fungal reproduction. In this study, we found varying degrees of prevalence for two distantly related genotypes (haplogroups) of Wolbachia and high degree of prevalence of Rhizobiales across colonies with little genetic variation. In addition, we found low occurrence of Ophiocordyceps. This study highlights a key first step in understanding the diversity, distribution, and prevalence of the microbial community of C. atratus.

Elucidating the biomineralization of low-temperature hydrothermal precipitates with varying Fe, Si contents: Indication from ultrastructure and microbiological analyses

Fe, Si-rich low-temperature hydrothermal precipitates, typical hydrothermal products of low-temperature diffuse flow, have been found widely on the seafloor. It is believed that microorganisms play an important role in the formation of Fe, Si-rich low-temperature precipitates, yet, microbial biomineralization within these precipitates has not been well understood. In this study, we characterized different hydrothermal precipitates collected from the Lau Basin of the western Pacific Ocean, using an integrated mineralogical, geochemical, ultrastructural and microbiological approach. Three types of Fe, Si-rich precipitates were identified: Fe-rich, Fe–Si-rich and Si-rich, consisting of amorphous or poor crystalline minerals, from the two-line ferrihydrite to opal-A. Geochemical indices suggest that the precipitates are typical low-temperature hydrothermal origin, precipitated from mixing, at various extent, of hydrothermal fluid and seawater. All three types of Fe, Si-rich precipitates show abundant and distinctive biogenic ultrastructures, indicating different biomineralization experiences. The Fe-rich precipitates dominantly exhibited the typical Fe-enriched ultrastructures produced by putative iron-oxidizing bacteria (FeOB), suggesting the prevalence of Fe-oxidation catalyzed by FeOB in its formation process. Similar FeOB-catalyzed biomineralization process also happened in Fe–Si-rich precipitates with the abundant occurrence of FeOB-induced ultrastructures. By contrast, the Si-enriched architectures, encompassing mycelium-like networks, became absolutely prevailing within Si-rich precipitates. Based on their indicative morphologies, mycelium-like networks were ascribed as silicified actinobacteria or fungi, suggesting that silicification induced by actinobacteria or fungi dominated the biomineralization process. Microbiological analysis revealed the existence of a series of diverse, heterogeneous microbial populations within different Fe, Si-rich precipitates. However, no putative FeOB lineages were detected in the Fe-rich and Fe–Si-rich precipitates. Taken together, our results indicate that different biomineralization processes induced by different microbial lineages contributed to the formation of the three different types of Fe, Si-rich precipitates and the distinct environmental conditions existed for heterogeneous microorganisms within these different Fe, Si-rich precipitates.

Genome of a Novel Bacterium "Candidatus Jettenia ecosi" Reconstructed From the Metagenome of an Anammox Bioreactor.

The microbial community of a laboratory-scale bioreactor based on the anammox process was investigated by using metagenomic approaches and fluorescent in situ hybridization (FISH). The bioreactor was initially inoculated with activated sludge from the denitrifying bioreactor of a municipal wastewater treatment station. By constantly increasing the ammonium and nitrite load, a microbial community containing the novel species of anammox bacteria “Candidatus Jettenia ecosi” developed in the bioreactor after 5 years when the maximal daily nitrogen removal rate reached 8.5 g/L. Sequencing of the metagenome of anammox granules and the binning of the contigs obtained, allowed a high quality draft genome of the dominant anammox bacterium, “Candidatus Jettenia ecosi” to be assembled. Annotation of the 3.9 Mbp long genome revealed 3970 putative protein-coding genes, 45 tRNA genes, and genes for 16S/23S rRNAs. Analysis of the genome of “Candidatus Jettenia ecosi” revealed genes involved in anammox metabolism, including nitrite and ammonium transporters, copper-containing nitrite reductase, a nitrate reductase complex, hydrazine synthase, and hydrazine dehydrogenase. Autotrophic carbon fixation could be accomplished through the Wood Ljungdahl pathway. The composition of the community was investigated through a search of 16S rRNA sequences in the metagenome and FISH analysis of the anammox granules. The presence of the members of Ignavibacteriae, Betaproteobacteria, Chloroflexi and other microbial lineages reflected the complexity of the microbial processes in the studied bioreactor performed by anammox Planctomycetes, fermentative bacteria, and denitrifiers.

Polymorphic Immune Mechanisms Regulate Commensal Repertoire

Environmental influences (infections and diet) strongly affect a host's microbiota. However, host genetics may influence commensal communities, as suggested by the greater similarity between the microbiomes of identical twins compared to non-identical twins. Variability of human genomes and microbiomes complicates the understanding of polymorphic mechanisms regulating the commensal communities. Whereas animal studies allow genetic modifications, they are sensitive to influences known as "cage" or "legacy" effects. Here, we analyze ex-germ-free mice of various genetic backgrounds, including immunodeficient and major histocompatibility complex (MHC) congenic strains, receiving identical input microbiota. The host's polymorphic mechanisms affect the gut microbiome, and both innate (anti-microbial peptides, complement, pentraxins, and enzymes affecting microbial survival) and adaptive (MHC-dependent and MHC-independent) pathways influence the microbiota. In our experiments, polymorphic mechanisms regulate only a limited number of microbial lineages (independently of their abundance). Our comparative analyses suggest that some microbes may benefit from the specific immune responses that they elicit.