Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons.

BACKGROUND: The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of any other mammal studied to date, raising key questions about the forces that shape the vaginal microbiome in non-human mammals. RESULTS: We used Illumina sequencing of the bacterial 16S rRNA gene to investigate variation in the taxonomic composition of the vaginal microbiota in 48 baboons (Papio cynocephalus), members of a well-studied wild population in Kenya. Similar to prior studies, we found that the baboon vaginal microbiota was not dominated by lactobacilli. Despite this difference, and similar to humans, reproductive state was the dominant predictor of baboon vaginal microbiota, with pregnancy, postpartum amenorrhea, and ovarian cycling explaining 18% of the variance in community composition. Furthermore, among cycling females, a striking 39% of variance in community composition was explained by ovarian cycle phase, with an especially distinctive microbial community around ovulation. Periovulatory females exhibited the highest relative abundance of lactic acid-producing bacteria compared to any other phase, with a mean relative abundance of 44%. To a lesser extent, sexual behavior, especially a history of shared sexual partners, also predicted vaginal microbial similarity between baboons. CONCLUSIONS: Despite striking differences in their dominant microbes, both human and baboon vaginal microbiota exhibit profound changes in composition in response to reproductive state, ovarian cycle phase, and sexual behavior. We found major shifts in composition during ovulation, which may have implications for disease risk and conception success. These findings highlight the need for future studies to account for fine-scale differences in reproductive state, particularly differences between the various phases of the ovarian cycle. Overall, our work contributes to an emerging understanding of the forces that explain intra- and inter-individual variation in the mammalian vaginal microbiome, with particular emphasis on its role in host health and disease risk.

Abundance and activity of vinyl chloride (VC)-oxidizing bacteria in a dilute groundwater VC plume biostimulated with oxygen and ethene.

Clean-up of vinyl chloride (VC)-contaminated groundwater could be enhanced by stimulating aerobic VC-oxidizing bacterial populations (e.g., methanotrophs) with amendments such as molecular oxygen. In addition, ethene gas injection could further stimulate a different group of aerobic ethene- and VC-oxidizing bacteria called "etheneotrophs." We estimated the abundance and activity of these different VC-oxidizing bacteria in portions of a dilute groundwater VC plume subjected to oxygen and ethene biostimulation. Pyrosequencing of 16S rRNA genes, amplified from community DNA extracted from five groundwater monitoring wells, revealed that Proteobacteria dominated the microbial community. Among the Proteobacteria, methanotroph relative abundance was 6.00 % (well RB52I), 2.81 % (well RB46D), 56.3 % (well RB58I), 23.8 % (well RB63I), and 2.57 % (well RB64I). Reverse transcription qPCR (RT-qPCR) analysis was used to determined methanotroph and etheneotroph functional gene expression from selected monitoring wells. Resulting transcript per gene ratios for methanotroph functional genes (pmoA and mmoX) were 0.013 (RB46D), 0.017 (RB63I), 0.112 (RB64I), and 0.004 (RB46D), 0.239 (RB63I), and 0.199 (RB64I), respectively. Transcript per gene ratios for etheneotroph functional genes (etnC and etnE) were 0.37 (RB46D), 0.81 (RB63I), 5.85 (RB64I), and 0.38 (RB46D), 0.67 (RB63I), and 2.28 (RB64I), respectively. When considered along with geochemical and contaminant data from these wells, our RT-qPCR results suggest that methanotrophs and etheneotrophs were participating in VC cometabolism. We conclude that these molecular diagnostic techniques could be helpful to site managers interested in documenting the effectiveness of VC bioremediation strategies.

Local-global overlap in diversity informs mechanisms of bacterial biogeography.

Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local-global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among 'patches', global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity.

Freshwater bacterial lifestyles inferred from comparative genomics.

While micro-organisms actively mediate and participate in freshwater ecosystem services, we know little about freshwater microbial genetic diversity. Genome sequences are available for many bacteria from the human microbiome and the ocean (over 800 and 200, respectively), but only two freshwater genomes are currently available: the streamlined genomes of Polynucleobacter necessarius ssp. asymbioticus and the Actinobacterium AcI-B1. Here, we sequenced and analysed draft genomes of eight phylogentically diverse freshwater bacteria exhibiting a range of lifestyle characteristics. Comparative genomics of these bacteria reveals putative freshwater bacterial lifestyles based on differences in predicted growth rate, capability to respond to environmental stimuli and diversity of useable carbon substrates. Our conceptual model based on these genomic characteristics provides a foundation on which further ecophysiological and genomic studies can be built. In addition, these genomes greatly expand the diversity of existing genomic context for future studies on the ecology and genetics of freshwater bacteria.

Diversity of the chlorite dismutase gene in low and high organic carbon rhizosphere soil colonized by perchlorate-reducing bacteria.

Chlorite dismutase (cld) is an essential enzyme in the biodegradation of perchlorate. The objective of this study was to determine the change in sequence diversity of the cld gene, and universal bacterial 16S rRNA genes, in soil samples under varying conditions of organic carbon, bioaugmentation, and plant influence. The cld gene diversity was not different between high organic carbon (HOC) and low organic carbon (LOC) soil. Combining results from HOC and LOC soil, diversity of the cld gene was decreased in soil that had been bioaugmented or planted. However, with both bioaugmentation and planting the cld diversity was not decreased. These observations were repeated when focusing on LOC soil. However, in HOC soil the cld diversity was not affected by reactor treatment. General bacterial diversity as measured with 16S rRNA was significantly greater in HOC soil than in LOC soil, but no significant difference was observed between reference soil and planted or bioaugmented soil. Different sequences of the cld gene occur in different species of microorganisms. In LOC soil, combining bioaugmentation and planting results in a highly diverse population of perchlorate degraders. This diverse population will be more resilient and is desirable where perchlorate reduction is a critical remediation process. Supplemental materials are available for this article. Go to the publisher's online edition of International Journal of Phytoremediation to view the supplemental file.

Microbial community dynamics during acetate biostimulation of RDX-contaminated groundwater.

Biostimulation of groundwater microbial communities (e.g., with carbon sources) is a common approach to achieving in situ bioremediation of organic pollutants (e.g., explosives). We monitored a field-scale approach to remediate the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in an aquifer near the Iowa Army Ammunition Plant in Middletown, IA. The purpose of the study was to gain insight into the effect of biostimulation on the microbial community. Biostimulation with acetate led to the onset of RDX reduction at the site, which was most apparent in monitoring well MW309. Based on previous laboratory experiments, we hypothesized that RDX degradation and metabolite production would correspond to enrichment of one or more Fe(III)-reducing bacterial species. Community DNA from MW309 was analyzed with 454 pyrosequencing and terminal restriction fragment length polymorphism. Production of RDX metabolites corresponded to a microbial community shift from primarily Fe(III)-reducing Betaproteobacteria to a community dominated by Fe(III)-reducing Deltaproteobacteria (Geobacteraceae in particular) and Bacteroidetes taxa. This data provides a firsthand field-scale microbial ecology context to in situ RDX bioremediation using modern sequencing techniques that will inform future biostimulation applications.

Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets.

Fungi are everywhere and interact with humans in countless ways, but a large group of fungi called 'Cryptomycota' has escaped detection until very recently. Still, the extent of diversity and ecological habits of this group remain largely unknown. We interrogated publically available 18S rRNA gene datasets, obtained via high-throughput sequencing from marine and freshwater samples, for Cryptomycota sequences. Contrary to previous work, we found evidence of substantial Cryptomycota diversity in the marine upper water column. Additionally, we produced a sequencing set from a groundwater aquifer, an environment unrepresented among 18S rRNA gene pyrosequencing sets. The Cryptomycota community in this aquifer sample appears distinct from the community in both freshwater and marine environments with evidence of a unique aquifer clade. This study significantly expands the boundary of known Cryptomycota sequence diversity and characterizes the phylogenetic distribution of this diversity in aquatic environments. Furthermore, the approach utilized is generalizable to discovery of novel micro-eukaryotic diversity from any lineage.