Buccal Swabbing as a Noninvasive Method To Determine Bacterial,Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.     

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

High throughput sequencing (HTSeq) of small ribosomal subunit amplicons has the potential for a comprehensive characterization of microbial community compositions, down to rare species. However, the error-prone nature of the multi-step experimental process requires that the resulting raw sequences are subjected to quality control procedures. These procedures often involve an abundance cutoff for rare sequences or clustering of sequences, both of which limit genetic resolution. Here we propose a simple experimental protocol that retains the high genetic resolution granted by HTSeq methods while effectively removing many low abundance sequences that are likely due to PCR and sequencing errors. According to this protocol, we split samples and submit both halves to independent PCR and sequencing runs. The resulting sequence data is graphically and quantitatively characterized by the discordance between the two experimental branches, allowing for a quick identification of problematic samples. Further, we discard sequences that are not found in both branches (“AmpliconDuo filter”). We show that the majority of sequences removed in this way, mostly low abundance but also some higher abundance sequences, show features expected from random modifications of true sequences as introduced by PCR and sequencing errors. On the other hand, the filter retains many low abundance sequences observed in both branches and thus provides a more reliable census of the rare biosphere. We find that the AmpliconDuo filter increases biological resolution as it increases apparent community similarity between biologically similar communities, while it does not affect apparent community similarities between biologically dissimilar communities. The filter does not distort overall apparent community compositions. Finally, we quantitatively explain the effect of the AmpliconDuo filter by a simple mathematical model.     

Specific Bacterial, Archaeal, and Eukaryotic Communities in Tidal-Flat Sediments along a Vertical Profile of Several Meters

The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as “tidal-flat cluster 1.” Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.     

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing protocols are, however, limited by the fraction of the 16S rRNA gene that is interrogated and therefore limit the resolution and quality of the profiling. To address this, we present the design of a novel protocol for shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to amplify more than 90% of sequences in the Greengenes database and with the ability to distinguish nearly twice as many species-level OTUs compared to existing protocols. Using several in silico and experimental datasets, we demonstrate that despite the presence of multiple variable and conserved regions, the resulting shotgun sequences can be used to accurately quantify the constituents of complex microbial communities. The reconstruction of a significant fraction of the 16S rRNA gene also enabled high precision (>90%) in species-level identification thereby opening up potential application of this approach for clinical microbial characterization.     

Spatial and Temporal Variation of Archaeal,Bacterial and Fungal Communities in Agricultural Soils

Background

Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.

Methodology/Principal Findings

In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.

Conclusions

Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.     

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.     

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities

Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities.     

Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs.     

Coincidental Loss of Bacterial Virulence in Multi-Enemy Microbial Communities

The coincidental virulence evolution hypothesis suggests that outside-host selection, such as predation, parasitism and resource competition can indirectly affect the virulence of environmentally-growing bacterial pathogens. While there are some examples of coincidental environmental selection for virulence, it is also possible that the resource acquisition and enemy defence is selecting against it. To test these ideas we conducted an evolutionary experiment by exposing the opportunistic pathogen bacterium Serratia marcescens to the particle-feeding ciliate Tetrahymena thermophila, the surface-feeding amoeba Acanthamoeba castellanii, and the lytic bacteriophage Semad11, in all possible combinations in a simulated pond water environment. After 8 weeks the virulence of the 384 evolved clones were quantified with fruit fly Drosophila melanogaster oral infection model, and several other life-history traits were measured. We found that in comparison to ancestor bacteria, evolutionary treatments reduced the virulence in most of the treatments, but this reduction was not clearly related to any changes in other life-history traits. This suggests that virulence traits do not evolve in close relation with these life-history traits, or that different traits might link to virulence in different selective environments, for example via resource allocation trade-offs.     

Layered Structure of Bacterial and Archaeal Communities and Their In Situ Activities in Anaerobic Granules

The microbial community structure and spatial distribution of microorganisms and their in situ activities in anaerobic granules were investigated by 16S rRNA gene-based molecular techniques and microsensors for CH₄, H₂, pH, and the oxidation-reduction potential (ORP). The 16S rRNA gene-cloning analysis revealed that the clones related to the phyla Alphaproteobacteria (detection frequency, 51%), Firmicutes (20%), Chloroflexi (9%), and Betaproteobacteria (8%) dominated the bacterial clone library, and the predominant clones in the archaeal clone library were affiliated with Methanosaeta (73%). In situ hybridization with oligonucleotide probes at the phylum level revealed that these microorganisms were numerically abundant in the granule. A layered structure of microorganisms was found in the granule, where Chloroflexi and Betaproteobacteria were present in the outer shell of the granule, Firmicutes were found in the middle layer, and aceticlastic Archaea were restricted to the inner layer. Microsensor measurements for CH₄, H₂, pH, and ORP revealed that acid and H₂ production occurred in the upper part of the granule, below which H₂ consumption and CH₄ production were detected. Direct comparison of the in situ activity distribution with the spatial distribution of the microorganisms implied that Chloroflexi contributed to the degradation of complex organic compounds in the outermost layer, H₂ was produced mainly by Firmicutes in the middle layer, and Methanosaeta produced CH₄ in the inner layer. We determined the effective diffusion coefficient for H₂ in the anaerobic granules to be 2.66 × 10⁻⁵ cm² s⁻¹, which was 57% in water.     

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity.     

Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing

The ability of rumen microorganisms to use fibrous plant matter plays an important role in ruminant animals; however, little information about rumen colonization by microbial populations after weaning has been reported. In this study, high-throughput sequencing was used to investigate the establishment of this microbial population in 80 to 110-day-old goats. Illumina sequencing of goat rumen samples yielded 101,356,610 nucleotides that were assembled into 256,868 reads with an average read length of 394 nucleotides. Taxonomic analysis of metagenomic reads indicated that the predominant phyla were distinct at different growth stages. The phyla Firmicutes and Synergistetes were predominant in samples taken from 80 to 100-day-old goats, but Bacteroidetes and Firmicutes became the most abundant phyla in samples from 110-day-old animals. There was a remarkable variation in the microbial populations with age; Firmicutes and Synergistetes decreased after weaning, but Bacteroidetes and Proteobacteria increased from 80 to 110 day of age. These findings suggested that colonization of the rumen by microorganisms is related to their function in the rumen digestive system. These results give a better understanding of the role of rumen microbes and the establishment of the microbial population, which help to maintain the host’s health and improve animal performance.     

Phylogenetic Diversity of Bacterial and Archaeal Communities in the Anoxic Zone of the Cariaco Basin

Microbial community samples were collected from the anoxic zone of the Cariaco Basin at depths of 320, 500, and 1,310 m on a November 1996 cruise and were used to construct 16S ribosomal DNA libraries. Of 60 nonchimeric sequences in the 320-m library, 56 belonged to the subdivision of the Proteobacteria (-Proteobacteria) and 53 were closely related to ectosymbionts of Rimicaris exoculata and Alvinella pompejana, which are referred to here as epsilon symbiont relatives (ESR). The 500-m library contained sequences affiliated with the fibrobacteria, the Flexibacter-Cytophaga-Bacteroides division, the division Verrucomicrobia, the division Proteobacteria, and the OP3 candidate division. The Proteobacteria included members of the γ, δ, and new candidate subdivisions, and γ-proteobacterial sequences were dominant (25.6%) among the proteobacterial sequences. As in the 320-m library, the majority of the -proteobacteria belonged to the ESR group. The genus Fibrobacter and its relatives were the second largest group in the library (23.6%), followed by the δ-proteobacteria and the -proteobacteria. The 1,310-m library had the greatest diversity; 59 nonchimeric clones in the library contained 30 unique sequences belonging to the planctomycetes, the fibrobacteria, the Flexibacter-Cytophaga-Bacteroides division, the Proteobacteria, and the OP3 and OP8 candidate divisions. The proteobacteria included members of new candidate subdivisions and the β, γ, δ, and -subdivisions. ESR sequences were still present in the 1,310-m library but in a much lower proportion (8.5%). One archaeal sequence was present in the 500-m library (2% of all microorganisms in the library), and eight archaeal sequences were present in the 1,310-m library (13.6%). All archaeal sequences fell into two groups; two clones in the 1,310-m library belonged to the kingdom Crenarchaeota and the remaining sequences in both libraries belonged to the kingdom Euryarchaeota. The latter group appears to be related to the Eel-TA1f2 sequence, which belongs to an archaeon suggested to be able to oxidize methane anaerobically. Based on phylogenetic inferences and measurements of dark CO₂ fixation, we hypothesized that (i) the ESR are autotrophic anaerobic sulfide oxidizers, (ii) sulfate reduction and fermentative metabolism may be carried out by a large number of bacteria in the 500- and 1,310-m libraries, and (iii) members of the Euryarchaeota found in relatively large numbers in the 1,310-m library may be involved in anaerobic methane oxidation. Overall, the composition of microbial communities from the Cariaco Basin resembles the compositions of communities from several anaerobic sediments, supporting the hypothesis that the Cariaco Basin water column is similar to anaerobic sediments.     

Archaeal and Bacterial Communities Respond Differently to Environmental Gradients in Anoxic Sediments of a California Hypersaline Lake,the Salton Sea

Sulfidic, anoxic sediments of the moderately hypersaline Salton Sea contain gradients in salinity and carbon that potentially structure the sedimentary microbial community. We investigated the abundance, community structure, and diversity of Bacteria and Archaea along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of Bacteria, Archaea, and Crenarchaeota. Community structure and diversity were evaluated by terminal restriction fragment length polymorphism (T-RFLP), quantitative analysis of gene (16S rRNA) frequencies of dominant microorganisms, and cloning and sequencing of 16S rRNA. Archaea were numerically dominant at all depths and exhibited a lesser response to environmental gradients than that of Bacteria. The relative abundance of Crenarchaeota was low (0.4 to 22%) at all depths but increased with decreased carbon content and increased salinity. Salinity structured the bacterial community but exerted no significant control on archaeal community structure, which was weakly correlated with total carbon. Partial sequencing of archaeal 16S rRNA genes retrieved from three sediment depths revealed diverse communities of Euryarchaeota and Crenarchaeota, many of which were affiliated with groups previously described from marine sediments. The abundance of these groups across all depths suggests that many putative marine archaeal groups can tolerate elevated salinity (5.0 to 11.8% [wt/vol]) and persist under the anaerobic conditions present in Salton Sea sediments. The differential response of archaeal and bacterial communities to salinity and carbon patterns is consistent with the hypothesis that adaptations to energy stress and availability distinguish the ecologies of these domains.The vast majority of cultured Archaea isolates are characterized as extremophiles, which thrive under environmental extremes of temperature, pH, salinity, and oxygen availability. Unlike Bacteria, these organisms are well defined by select physiologies or catabolic activities. Cultivated halophilic archaea are obligate aerobes, and with a few exceptions (58), most 16S rRNA gene sequences affiliated with this physiological group have been recovered primarily from environments with oxygen present. Thermophilic archaea, many of which utilize hydrogen-based metabolisms, have temperature requirements that preclude their survival and growth in more moderate environments. Other archaeal physiological groups include acidophiles, which thrive in acidic and mostly high-temperature environments, the obligate anaerobic methanogens, which are capable of competing with Bacteria when more energetically favorable electron acceptors are not available (i.e., sulfate), and methane-oxidizing archaea, which require methane for energy production. Recent work on several Crenarchaeota isolates points to nitrification as their primary energy metabolism, but these organisms have been detected in cold, predominantly aerobic environments, such as open ocean waters and soil (47), and in hyperthermophilic environments (24).Several archaeal groups identified using only 16S rRNA genes, for which no current isolates exist, have been detected in anaerobic sediments of the marine subsurface (6), estuaries (42), freshwater (46), and salt lakes (29). While their physiology and catabolism remain a source of speculation, the environmental distribution patterns of these mesophilic, presumably anaerobic, groups seemingly exclude the physiological and catabolic types outlined above. That is, the persistence of diverse archaeal populations in anoxic sediments at moderate temperature and salinity and at circumneutral pH with only trace levels of methane strongly suggests that alternative metabolic or physiological activities must characterize these populations.Saline lakes are ubiquitous and can be found on all continents. Although many saline lakes are labeled “extreme” environments, microbial diversity within their sediments is often equivalent to that reported for studies of freshwater and marine systems (28). Most studies of the microbial ecology within saline lakes have focused on gradients within the water column, with very few studies on patterns within the sediments. Specifically, these studies have examined how changes in water column salinity lead to shifts in microbial productivity and diversity (8). However, particle-associated microbial communities are known to differ fundamentally from water column or free-living populations (1, 18). These observed differences could be explained by the type and strength of environmental gradients that microbial communities in sediments experience, as opposed to those encountered by pelagic communities.Sediments contain strong environmental gradients, such as time (e.g., sediment age at depth), nutrient and carbon availability, and the dominant terminal electron-accepting process (TEAP) resulting from the sequential use of available oxidants by the microbial community (41). These gradients can lead to changes in the dominant microbial groups (i.e., a shift from sulfate reducers to methanogens with depth and age). Many saline lakes are highly productive and shallow and experience large fluctuations in water level due to climatic changes or to changes in inflows due to urban and agricultural activities. Changes in lake level can lead to dramatic shifts in mixing regimens, nutrient cycling, and water chemistry. Historic fluctuations in water column salinity are often recorded within the sediments in the form of evaporite deposits, which may act as additional sources of ionic loading of the water column (62). These sedimentary salinity gradients may modulate the metabolic activity of some microbial groups. For example, Oren (44) proposed bioenergetic constraints as a possible explanation for the reduced activity or absence of some microbial groups within high-salinity environments. Thus, saline lake sediments are excellent natural laboratories in which to study changes and adaptations of microbial communities due to large-scale changes in environmental gradients.The Salton Sea is a large (980 km²), eutrophic, moderately hypersaline (48 to 50 g liter⁻¹), terminal lake located 69 m below sea level in the Salton Basin, CA. Several large lakes have formed in the Salton Basin over geologic history, the most recent of which was Lake Cahuilla ca. 300 years ago (7). The current lake was unintentionally created in 1905-1907, when the Colorado River flooded the Salton Basin for a period of 16 months. Profundal sediments are highly sulfidic, and sulfate reduction is suspected to be the dominant TEAP within these sediments (54). Based on elemental analysis (51) and ¹³⁷Cs activity (37) of sediment layers, a depth of ∼22 cm marks the point when flooding of the Salton Basin occurred. Sediment above this depth represents the ca. 102 years of historical change within the Salton Sea, including a shift from a water column salinity of 35 g liter⁻¹ to the hypersaline conditions that currently exist. Sediments below this depth consist of low-carbon, gypsum-rich evaporite deposits that were present on the older dry lake bed prior to the formation of the current lake. A previous study reported several strong geochemical gradients within pore water across this relatively small depth range (62).In this work, a suite of cultivation-independent techniques and geochemical analyses was utilized to correlate shifts in abundance, community structure, and diversity of Archaea and Bacteria in Salton Sea sediments with changes in environmental gradients. Large differences in abundance and community structure patterns of Archaea and Bacteria were found along the gradients. In addition, the majority of archaeal sequences retrieved were affiliated with previously described but as yet uncultivated groups identified from various marine sedimentary environments. This indicates that these groups are able to tolerate the higher salinity and anaerobic conditions characteristic of Salton Sea sediments. Fundamental differences between the metabolic capacities and ecologies of Archaea and Bacteria are discussed to explain these patterns.     

Termite Hindguts and the Ecology of Microbial Communities in the Sequencing Age

Advances in high‐throughput nucleic acid sequencing have improved our understanding of microbial communities in a number of ways. Deeper sequence coverage provides the means to assess diversity at the resolution necessary to recover ecological and biogeographic patterns, and at the same time single‐cell genomics provides detailed information about the interactions between members of a microbial community. Given the vastness and complexity of microbial ecosystems, such analyses remain challenging for most environments, so greater insight can also be drawn from analysing less dynamic ecosystems. Here, we outline the advantages of one such environment, the wood‐digesting hindgut communities of termites and cockroaches, and how it is a model to examine and compare both protist and bacterial communities. Beyond the analysis of diversity, our understanding of protist community ecology will depend on using statistically sound sampling regimes at biologically relevant scales, transitioning from discovery‐based to experimental ecology, incorporating single‐cell microbiology and other data sources, and continued development of analytical tools.