Insights and inferences about integron evolution from genomic data

Research articl

Microbes as engines of ecosystem function : When does community structure enhance predictions of ecosystem processes?

FUNDING This work was supported by NSF grant DEB-1221215 to DN, as well as grants supporting the generation of our datasets as acknowledged in their original publications and in Supplementary Table S1. ACKNOWLEDGMENT We thank the USGS Powell Center ‘Next Generation Microbes’ working group, anonymous reviews, Brett Melbourne, and Alan Townsend for valuable feedback on this project.Peer reviewedPublisher PD

Direct sequencing of the human microbiome readily reveals community differences

Future sequencing of the human microbiota will require greater breadth rather than depth

Carbon, Metals, and Grain Size Correlate with Bacterial Community Structure in Sediments of a High Arsenic Aquifer

Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As). This has globally important implications since As in drinking water affects the health of over 100 million people worldwide, including in the Ganges–Brahmaputra Delta region of Bangladesh where geogenic arsenic in groundwater can reach concentrations of more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across gradients in sediment texture and chemistry in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flow path at a range of depths between 1.5 and 15 m. We identified significant differences in bacterial community composition between locations in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C), manganese (Mn), and iron (Fe) concentrations. Deltaproteobacteria and Chloroflexi were found in higher proportions in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were in higher proportions in sandy sediments with lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance-reducers in the high C and metal sediments. It is well-documented that C, Mn, and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community

Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria

Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 grams of volcanic material, and using whole genome shotgun sequencing, observed only 75 - 78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9% - 98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56% - 72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions

The causes and consequences of microbial community structure

The causes and consequences of differences in microbial community structure, defined here as the relative proportions of rare and abundant organisms within a community, are poorly understood. Articles in "The Causes and Consequences of Microbial Community Structure", use empirical or modeling approaches as well as literature reviews to enrich our mechanistic understanding of the controls over the relationship between community structure and ecosystem processes. Specifically, authors address the role of trait distributions and tradeoffs, species-species interactions, evolutionary dynamics, community assembly processes and physical controls in affecting ‘who’s there’ and ‘what they are doing’

Inoculation, Growth and Bactericidal Effects of Three Kombucha Cultures

Kombucha, a domesticated consortium of several microorganisms grown on sugared tea, has been valued as a nutritive health aid for over a millennium. In this study, three cultures of kombucha were obtained from diverse sources. Different inoculation methods were compared, and the wet and dry weights of the nascent pellicles were measured when cultured on several carbon sources. In addition, the anti-bacterial properties of the fermented kombucha teas were tested against Escherichia coli and Staphylococcus epidermis. Inoculation with macerated pellicles gave the fastest kombucha growth. The best carbon sources for growth of the nascent kombucha pellicles were sucrose, glucose, and fructose. On maltose, galactose, and lactose, not only did the kombucha pellicles grow poorly but 25% were also contaminated by common airborne molds. Good growth of the kombucha cultures was correlated with low pH of the fermented tea. Antibacterial effects of concentrated fermented teas and vinegar were similar to those of 1 mmol ampicillin against Escherichia coli or 0.01 mmol penicillin against Staphylococcus epidermis. When the pH of concentrated kombucha teas was neutralized, their bactericidal effects were no better than unfermented controls

Soil bacterial community structure remains stable over a five-year chronosequence of insect-induced tree mortality

Extensive tree mortality from insect epidemics has raised concern over possible effects on soil biogeochemical processes. Yet despite the importance of microbes in biogeochemical processes, how soil bacterial communities respond to insect-induced tree mortality is largely unknown. We examined soil bacterial community structure (via 16S rRNA pyrosequencing) and community assembly processes (via null deviation analysis) along a five-year chronosequence (substituting space for time) of bark beetle-induced tree mortality in the southern Rocky Mountains, USA. We also measured soil microbial biomass and soil chemistry, and used in situ experiments to assess inorganic nitrogen mineralization rates. We found that bacterial community structure and assembly―which was strongly influenced by stochastic processes―were largely unaffected by tree mortality despite increased soil ammonium (NH4+) pools and reductions in soil nitrate (NO3-) pools and net nitrogen mineralization rates after tree mortality. Linear models suggested that microbial biomass and bacterial phylogenetic diversity are significantly correlated with nitrogen mineralization rates of this forested ecosystem. However, given the overall resistance of the bacterial community to disturbance from tree mortality, soil nitrogen processes likely remained relatively stable following tree mortality when considered at larger spatial and longer temporal scales—a supposition supported by the majority of available studies regarding biogeochemical effects of bark beetle infestations in this region. Our results suggest that soil bacterial community resistance to disturbance helps to explain the relatively weak effects of insect-induced tree mortality on soil N and C pools reported across the Rocky Mountains, USA