Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring.

Alkaline sulfide-rich hot springs provide a unique environment for microbial community and arsenic (As) biogeochemistry. In this study, a representative alkaline sulfide-rich hot spring, Zimeiquan in the Tengchong geothermal area, was chosen to study arsenic geochemistry and microbial community using Illumina MiSeq sequencing. Over 0.26 million 16S rRNA sequence reads were obtained from 5-paired parallel water and sediment samples along the hot spring's outflow channel. High ratios of As(V)/AsSum (total combined arsenate and arsenite concentrations) (0.59-0.78), coupled with high sulfide (up to 5.87 mg/L), were present in the hot spring's pools, which suggested As(III) oxidation occurred. Along the outflow channel, AsSum increased from 5.45 to 13.86 μmol/L, and the combined sulfide and sulfate concentrations increased from 292.02 to 364.28 μmol/L. These increases were primarily attributed to thioarsenic transformation. Temperature, sulfide, As and dissolved oxygen significantly shaped the microbial communities between not only the pools and downstream samples, but also water and sediment samples. Results implied that the upstream Thermocrinis was responsible for the transformation of thioarsenic to As(III) and the downstream Thermus contributed to derived As(III) oxidation. This study improves our understanding of microbially-mediated As transformation in alkaline sulfide-rich hot springs

Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China's grasslands.

Patterns of variation in plant and animal diversity along precipitation gradients have been extensively studied, but much less is known about how and to what extent precipitation affects the biogeographic distribution of microbial diversity in arid areas across large spatial scales. Here we collected soils from 54 sites along a 3700 km transect covering a wide range of grassland ecosystems with distinct aridity gradients. We quantified the bacterial community diversity and the effects of climate, edaphic parameter and geographic distance on the bacterial community structure using high-throughput 16S rRNA gene sequencing. Of the 35 phyla detected, 6 were dominant: Actinobacteria, Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes and Planctomycetes. Aridity was a major factor influencing bacterial diversity, community composition and taxon abundance. Although the pattern of bacterial species richness is markedly different from that of plant species richness, most soil bacteria were endemic to particular bioregions like macro-organisms. Community similarity significantly declined with environmental distance and geographic distance (r = -0.579 and -0.773, respectively). Geographic distance (historical contingencies) contributed more to bacterial community variation (36.02%) than combined environmental factors (24.06%). Overall, our results showed that geographic distance and climatic factors concurrently govern bacterial biogeographic patterns in arid and semi-arid grassland

Elevated CO2 and Warming Altered Grassland Microbial Communities in Soil Top-Layers.

As two central issues of global climate change, the continuous increase of both atmospheric CO2 concentrations and global temperature has profound effects on various terrestrial ecosystems. Microbial communities play pivotal roles in these ecosystems by responding to environmental changes through regulation of soil biogeochemical processes. However, little is known about the effect of elevated CO2 (eCO2) and global warming on soil microbial communities, especially in semiarid zones. We used a functional gene array (GeoChip 3.0) to measure the functional gene composition, structure, and metabolic potential of soil microbial communities under warming, eCO2, and eCO2 + warming conditions in a semiarid grassland. The results showed that the composition and structure of microbial communities was dramatically altered by multiple climate factors, including elevated CO2 and increased temperature. Key functional genes, those involved in carbon (C) degradation and fixation, methane metabolism, nitrogen (N) fixation, denitrification and N mineralization, were all stimulated under eCO2, while those genes involved in denitrification and ammonification were inhibited under warming alone. The interaction effects of eCO2 and warming on soil functional processes were similar to eCO2 alone, whereas some genes involved in recalcitrant C degradation showed no significant changes. In addition, canonical correspondence analysis and Mantel test results suggested that NO3-N and moisture significantly correlated with variations in microbial functional genes. Overall, this study revealed the possible feedback of soil microbial communities to multiple climate change factors by the suppression of N cycling under warming, and enhancement of C and N cycling processes under either eCO2 alone or in interaction with warming. These findings may enhance our understanding of semiarid grassland ecosystem responses to integrated factors of global climate change

Geochip: A high throughput genomic tool for linking community structure to functions

GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial community structure. However, several challenges remain regarding the development and applications of microarrays for microbial community analysis

Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes

Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO3--N and P concentrations. The microbial taxa-area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m(2), which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies

Microbial functional traits are sensitive indicators of mild disturbance by lamb grazing.

Mild disturbances are prevalent in the environment, which may not be easily notable but could have considerable ecological consequences over prolonged periods. To evaluate this, a field study was designed to examine the effects of very light-intensity lamb grazing on grassland soil microbiomes with different soil backgrounds. No significant change (P > 0.05) was observed in any vegetation and soil variables. Nonetheless, hundreds of microbial functional gene families, but not bacterial taxonomy, were significantly (P < 0.05) shifted. The relative abundances of both taxonomic markers and functional genes related to nitrifying bacteria were also changed. The observation highlighted herein, showing a high level of sensitivity with respect to functional traits (functionally categorized taxa or genes) in differentiating mild environmental disturbance, suggests that the key level at which to address microbial responses may not be "species" (by means of rRNA taxonomy), but rather at the functional gene level

A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom.

Phytoplankton blooms are a worldwide problem and can greatly affect ecological processes in aquatic systems, but its impacts on the functional potential of microbial communities are limited. In this study, a high-throughput microarray-based technology (GeoChip) was used to profile the functional potential of free-living microbes from the Xiamen Sea Area in response to a 2011 Akashiwo sanguinea bloom. The bloom altered the overall community functional structure. Genes that were significantly (p < 0.05) increased during the bloom included carbon degradation genes and genes involved in nitrogen (N) and/or phosphorus (P) limitation stress. Such significantly changed genes were well explained by chosen environmental factors (COD, nitrite-N, nitrate-N, dissolved inorganic phosphorus, chlorophyll-a and algal density). Overall results suggested that this bloom might enhance the microbial converting of nitrate to N2 and ammonia nitrogen, decrease P removal from seawater, activate the glyoxylate cycle, and reduce infection activity of bacteriophage. This study presents new information on the relationship of algae to other microbes in aquatic systems, and provides new insights into our understanding of ecological impacts of phytoplankton blooms