Recently Deglaciated High-Altitude Soils of the Himalaya: Diverse Environments, Heterogenous Bacterial Communities and Long-Range Dust Inputs from the Upper Troposphere

<div><p>Background</p><p>The Himalaya with its altitude and geographical position forms a barrier to atmospheric transport, which produces much aqueous-particle monsoon precipitation and makes it the largest continuous ice-covered area outside polar regions. There is a paucity of data on high-altitude microbial communities, their native environments and responses to environmental-spatial variables relative to seasonal and deglaciation events.</p><p>Methodology/Principal Findings</p><p>Soils were sampled along altitude transects from 5000 m to 6000 m to determine environmental, spatial and seasonal factors structuring bacterial communities characterized by 16 S rRNA gene deep sequencing. Dust traps and fresh-snow samples were used to assess dust abundance and viability, community structure and abundance of dust associated microbial communities. Significantly different habitats among the altitude-transect samples corresponded to both phylogenetically distant and closely-related communities at distances as short as 50 m showing high community spatial divergence. High within-group variability that was related to an order of magnitude higher dust deposition obscured seasonal and temporal rearrangements in microbial communities. Although dust particle and associated cell deposition rates were highly correlated, seasonal dust communities of bacteria were distinct and differed significantly from recipient soil communities. Analysis of closest relatives to dust OTUs, HYSPLIT back-calculation of airmass trajectories and small dust particle size (4–12 µm) suggested that the deposited dust and microbes came from distant continental, lacustrine and marine sources, e.g. Sahara, India, Caspian Sea and Tibetan plateau. <i>Cyanobacteria</i> represented less than 0.5% of microbial communities suggesting that the microbial communities benefitted from (co)deposited carbon which was reflected in the psychrotolerant nature of dust-particle associated bacteria.</p><p>Conclusions/Significance</p><p>The spatial, environmental and temporal complexity of the high-altitude soils of the Himalaya generates ongoing disturbance and colonization events that subject heterogeneous microniches to stochastic colonization by far away dust associated microbes and result in the observed spatially divergent bacterial communities.</p></div

Soluble Electron Shuttles Can Mediate Energy Taxis toward Insoluble Electron Acceptors

<i>Shewanella</i> species grow in widely disparate environments and play key roles in elemental cycling, especially in environments with varied redox conditions. To obtain a system-level understanding of <i>Shewanella’s</i> robustness and versatility, the complex interplay of cellular growth, metabolism, and transport under conditions of limiting carbon sources, energy sources, and electron acceptors must be elucidated. In this paper, population-level taxis of <i>Shewanella oneidensis</i> MR-1 cells in the presence of a rate-limiting, insoluble electron acceptor was investigated. A novel mechanism, mediated energy taxis, is proposed by which <i>Shewanella</i> use riboflavin as both an electron shuttle and an attractant to direct cell movement toward local sources of insoluble electron acceptors. The cells secrete reduced riboflavin, which diffuses to a nearby particle containing an insoluble electron acceptor and is oxidized. The oxidized riboflavin then diffuses away from the particle, establishing a spatial gradient that draws cells toward the particle. Experimental and modeling results are presented to support this mechanism. <i>S. oneidensis</i> MR-1 cells inoculated into a uniform dispersion of MnO₂ particles in dilute agar exhibited taxis outward, creating a clear zone within which riboflavin was detected by mass spectrometry. Cells inoculated into dilute agar containing oxidized riboflavin similarly exhibited taxis, rapidly forming an expanding zone of reduced riboflavin. A mathematical model based on the proposed mechanism was able to predict experimental trends, including how concentrations of riboflavin and insoluble electron acceptors (e.g., MnO₂) affected tactic cell migration

Non-metric multidimensional scaling ordination of 6000 m microbial communities sampled in autumn of 2002 (▾), 2005 (▪) and in spring 2006 (•) next to corresponding 2005 autumn (□) and spring 2006 (○) dust samples.

<p>Note - no significant groups could be identified using NP-MANOVA (0.05</p

Non-metric multidimensional scaling ordination of 5000–6000 m altitudinal gradient soil characteristics.

<p>(•) 6000 m, (▴) 5800 m, (×) 5600 m, (_*) 5400 m, (+) 5200 m, (▪) 5000 m. Individual samples connected by lines define convex hull surface area of NM-MDS scores of environmental characteristics as a measure of trait-space covered.</p

Conditional effects of environmental variables selected by forward selection in redundancy analysis (RDA) as determined by 4999 Monte Carlo permutations under the full multivariate model at the three taxonomic levels.

<p>Only the relevant environmental factors are listed.</p

Distance-decay relationships in the non-continuous permafrost soils of the 1000 m altitude gradient.

<p>Pairwise dissimilarities (Bray-Curtis index) of microbial communities were plotted as a function of the distance (vertical plus horizontal) between the sampling locations.</p

The relationship between dust particle number and microbial abundance during 2002, 2005 and 2006 sampling campaigns.

<p>(•) 6000 m, (▴) 5800 m, (□) 5600 m, (○) 5400 m, (?) 5200 m, (▪) 5000 m. () 6000 m autumn 2005; () 6000 m spring 2006.</p

Non-metric multidimensional scaling ordination of microbial communities sampled from 5000–6000 m altitudinal gradient.

<p>(•) 6000 m, (▴) 5800 m, (×) 5600 m, (_*) 5400 m, (+) 5200 m, (▪) 5000 m. Horizontal transect formed significant groups (NP-MANOVA, p<0.05). Filled symbols denote barren soils. Individual samples connected by lines define convex hull surface area of NM-MDS scores of microbial community characteristics as a measure of community-space covered.</p

Variance partitioning of environmental and spatial factors shaping microbial communities at the three phylogenetic levels (OTU, Order, Phylum).

<p>Variance partitioning of environmental and spatial factors shaping microbial communities at the three phylogenetic levels (OTU, Order, Phylum).</p

Genomic Diversity of <em>Escherichia</em> Isolates from Diverse Habitats

<div><p>Our understanding of the <em>Escherichia</em> genus is heavily biased toward pathogenic or commensal isolates from human or animal hosts. Recent studies have recovered <em>Escherichia</em> isolates that persist, and even grow, outside these hosts. Although the environmental isolates are typically phylogenetically distinct, they are highly related to and phenotypically indistinguishable from their human counterparts, including for the coliform test. To gain insights into the genomic diversity of <em>Escherichia</em> isolates from diverse habitats, including freshwater, soil, animal, and human sources, we carried out comparative DNA-DNA hybridizations using a multi-genome <em>E. coli</em> DNA microarray. The microarray was validated based on hybridizations with selected strains whose genome sequences were available and used to assess the frequency of microarray false positive and negative signals. Our results showed that human fecal isolates share two sets of genes (n>90) that are rarely found among environmental isolates, including genes presumably important for evading host immune mechanisms (e.g., a multi-drug transporter for acids and antimicrobials) and adhering to epithelial cells (e.g., hemolysin E and fimbrial-like adhesin protein). These results imply that environmental isolates are characterized by decreased ability to colonize host cells relative to human isolates. Our study also provides gene markers that can distinguish human isolates from those of warm-blooded animal and environmental origins, and thus can be used to more reliably assess fecal contamination in natural ecosystems.</p> </div