Isotopic and genetic methods reveal the role of the gut microbiome in mammalian host essential amino acid metabolism.

Intestinal microbiota perform many functions for their host, but among the most important is their role in metabolism, especially the conversion of recalcitrant biomass that the host is unable to digest into bioavailable compounds. Most studies have focused on the assistance gut microbiota provide in the metabolism of carbohydrates, however, their role in host amino acid metabolism is poorly understood. We conducted an experiment on Mus musculus using 16S rRNA gene sequencing and carbon isotope analysis of essential amino acids (AAESS) to quantify the community composition of gut microbiota and the contribution of carbohydrate carbon used by the gut microbiome to synthesize AAESS that are assimilated by mice to build skeletal muscle tissue. The relative abundances of Firmicutes and Bacteroidetes inversely varied as a function of dietary macromolecular content, with Firmicutes dominating when mice were fed low-protein diets that contained the highest proportions of simple carbohydrates (sucrose). Mixing models estimated that the microbial contribution of AAESS to mouse muscle varied from less than 5% (threonine, lysine, and phenylalanine) to approximately 60% (valine) across diet treatments, with the Firmicute-dominated microbiome associated with the greatest contribution. Our results show that intestinal microbes can provide a significant source of the AAESS their host uses to synthesize structural tissues. The role that gut microbiota play in the amino acid metabolism of animals that consume protein-deficient diets is likely a significant but under-recognized aspect of foraging ecology and physiology

Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem.

Primary production is the fundamental source of energy to foodwebs and ecosystems, and is thus an important constraint on soil communities. This coupling is particularly evident in polar terrestrial ecosystems where biological diversity and activity is tightly constrained by edaphic gradients of productivity (e.g., soil moisture, organic carbon availability) and geochemical severity (e.g., pH, electrical conductivity). In the McMurdo Dry Valleys of Antarctica, environmental gradients determine numerous properties of soil communities and yet relatively few estimates of gross or net primary productivity (GPP, NPP) exist for this region. Here we describe a survey utilizing pulse amplitude modulation (PAM) fluorometry to estimate rates of GPP across a broad environmental gradient along with belowground microbial diversity and decomposition. PAM estimates of GPP ranged from an average of 0.27 μmol

Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale

Understanding controls over the distribution of soil bacteria is a fundamental Understanding controls over the distribution of soil bacteria is a fundamental step toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when determining the controls on soil microbial community characteristics. toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when determining the controls on soil microbial community characteristics

Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages.

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal ‘filamentous streamer’ communities (~40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circumneutral pH (6.5 - 7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circumneutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl CoA synthetase (Ccs) and citryl CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales

16S rRNA Phylogenetic Investigation of the Candidate Division “Korarchaeota”

The environmental distribution and phylogeny of “Korarchaeota,” a proposed ancient archaeal division, was investigated by using the 16S rRNA gene framework. Korarchaeota-specific primers were designed based on previously published sequences and used to screen a variety of environments. Korarchaeota 16S rRNA genes were amplified exclusively from high temperature Yellowstone National Park hot springs and a 9°N East Pacific Rise deep-sea hydrothermal vent. Phylogenetic analyses of these and all available sequences suggest that Korarchaeota exhibit a high level of endemicity

Archaeal Ecology

11 pages, 4 figuresThe Archaea represent one of the three domains of life and are distinguished from the Bacteria and Eukarya both phylogenetically and biochemically. As a group, the Archaea are physiologically diverse and inhabit a wide range of ecosystems, including the most extreme environments on Earth. While traditionally thought to be restricted to just a few phyla and primarily inhabiting extreme environments, Archaea are now known to be globally distributed across many environments and of significant importance in multiple biogeochemical cycles. The Archaea also comprise a phylogenetically and metabolically diverse group of organisms in several recognised phyla and many more recently proposed phylum-level lineages representing uncultivated organisms. The use of environmental genomics to understand uncultured archaeal diversity has recently shed light on many new potential lineages of Archaea and continues to expand and revise our understanding of Archaea in natural environmentsPeer Reviewe

Impact of commercial natural gas production on geochemistry and microbiology in a shale-gas reservoir

We consider the effect that commercial gas production has had on microbiology and water and gas geochemistry in the northern producing trend of the Antrim Shale, an unconventional gas reservoir in the Michigan Basin, USA. We analyzed gas, water, and microbial biomass samples collected from seven wells in 2009 and compared our findings to the result of analyses performed as early as 1991 on samples collected from the same wells. We also examined production records associated with six wells. Water production has decreased sharply over time and is currently at 0.2 to 14.6% of peak levels. While this has happened, the chemical and isotopic composition of gas and water produced from the wells has shifted. The proportion of CO[subscript 2] has increased by as much as 15 mole% while CH[subscript 4] content has correspondingly decreased. Isotopically, the δ[superscript 13]C and δD values of CH[subscript 4] decreased for most wells by averages of 1.3‰ and 9‰, respectively, while δ[superscript 13]C values of CO[subscript 2] increased for most wells by an average of 1.7‰. Alkalinity in the water from each well decreased by 10 mM on average and SO[subscript 4][superscript 2−] content increased from below 50 μM to over 200 μM on average in water from each well with initial values. Microorganisms most closely related to CO[subscript 2]-reducing methanogens were the most abundant group in archaeal clone libraries and SO[subscript 4][superscript 2−] reducers were the most abundant group in bacterial libraries. In contrast, no SO[subscript 4][superscript 2−] reducers were identified in a nucleic acid-based analysis of a sample collected in 2002 from one of the wells we sampled . Our results show that commercial gas production has not only caused chemical and isotopic changes in water and gas in the Antrim Shale but also an increase in the abundance of SO[subscript 4][superscript 2−]-reducing microorganisms, a change that can ultimately have a negative impact on biogenic CH[subscript 4] formation. Processes that can explain these changes include ongoing biogeochemical reactions, groundwater flow, gas desorption, and open-system degassing

Core OTUs across 75% of all 60 snail samples.

<p>Core OTUs across 75% of all 60 snail samples.</p

Knox et al. data

Full dataset for Knox et al. (2017) Ecology Letter

Results from random forests classifiers.

<p>Results from random forests classifiers.</p