Humid tropical leguminous tree and pasture grass responsiveness to vesicular-arbuscular mycorrhizal infection

Phosphorus is the major nutrient limiting plant growth in a Costa Rican silvopastoral system located on an acid, high P-retaining, volcanic soil. We investigated plant responsiveness to vesicular-arbuscular mycorrhizal (VAM) inoculation using the leguminous tree species Erythrina berteroana Urban, and the two dominant grass species Paspalum conjugatum Berg and Homolepsis aturensis Chase of this silvopastoral system. We grew grass seedlings in the greenhouse for 15 weeks in a methyl bromide-sterilized study soil to which either mixed-species VAM inoculum (Theobroma cacao feeder roots) or autoclave-sterilized cacao roots (non-inoculated control) were added. E. berteroana was grown from both seedlings and vegetative stakes (40 cm long) for 30 and 19 weeks, respectively. Upon harvest, we measured above and below ground biomass, N and P content, rootshoot ratio, legume nodulation, and VAM infection levels. The total above-ground and root biomass of mycorrhizae-inoculated P. conjugatum seedlings were 2.5 and 2.8 times greater than those of noninoculated seedlings. In contrast, VAM-inoculated seedlings of H. aturensis produced 8.4 and 5.9 times more total above-ground and root mass than noninoculated seedlings. Mycorrhizae-inoculated E. berteroana seedlings produced 10.6 times greater shoot biomass for inoculated versus noninoculated seedlings, while E. berteroana vegetative stakes exhibited a negative growth response to VAM inoculation (an approximately 16% decrease in shoot biomass for VAM-inoculated cuttings). The difference in responsiveness between Erythrina growth forms is hypothesized to reflect the cost-benefit relationship between plant host and fungal symbiont for energy and nutrient reserves.     

Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux

A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO(2) flux was measured at tillering (S1), grain filling (S2) and ripening (S3) across the growth stages. Microbial community structure, abundance and activity were analyzed using a combination of functional (enzymes) and denaturing gradient gel electrophoresis (DGGE) and real-time PCR molecular approaches. Invertase and urease activities, total microbial biomass carbon, bacterial 16S rRNA and fungal internal transcribed spacer rRNA gene copies were found to be the highest at S2 under both cultivars, being greater under the hybrid cultivar than under the conventional cultivar across the stages. Moreover, the CO(2) flux was 11%, 16% and 25% higher under the hybrid cultivar than under the conventional cultivar at S1, S2 and S3, respectively. Principal component analyses of the PCR-DGGE profile revealed a significant difference between conventional and hybrid cultivars across growth stages. Sequencing DGGE bands of the bacterial 16S rRNA gene showed that a particular bacterial group of Alphaproteobacteria was enhanced and several distinct operational taxonomic units markedly resembled Ascomycota under the hybrid cultivar. These illustrate a significant selection of a particular group of bacteria and fungi of the hybrid cultivar. However, the potential impacts of these cultivar effects in soil C and N cycling deserve further field studies.     

Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds

The bacterial and fungal rhizosphere communities of strawberry (Fragaria ananassa Duch.) and oilseed rape (Brassica napus L.) were analysed using molecular fingerprints. We aimed to determine to what extent the structure of different microbial groups in the rhizosphere is influenced by plant species and sampling site. Total community DNA was extracted from bulk and rhizosphere soil taken from three sites in Germany in two consecutive years. Bacterial, fungal and group-specific (Alphaproteobacteria, Betaproteobacteria and Actinobacteria) primers were used to PCR-amplify 16S rRNA and 18S rRNA gene fragments from community DNA prior to denaturing gradient gel electrophoresis (DGGE) analysis. Bacterial fingerprints of soil DNA revealed a high number of equally abundant faint bands, while rhizosphere fingerprints displayed a higher proportion of dominant bands and reduced richness, suggesting selection of bacterial populations in this environment. Plant specificity was detected in the rhizosphere by bacterial and group-specific DGGE profiles. Different bulk soil community fingerprints were revealed for each sampling site. The plant species was a determinant factor in shaping similar actinobacterial communities in the strawberry rhizosphere from different sites in both years. Higher heterogeneity of DGGE profiles within soil and rhizosphere replicates was observed for the fungi. Plant-specific composition of fungal communities in the rhizosphere could also be detected, but not in all cases. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Rostock site revealed that Streptomyces sp. and Rhizobium sp. were among the dominant ribotypes in the strawberry rhizosphere, while sequences from Arthrobacter sp. corresponded to dominant bands from oilseed rape bacterial fingerprints.     

Plant-associated fungi support bacterial resilience following water limitation

Drought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H₂¹⁸O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater in R. irregularis compared to S. bescii-inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought susceptible. Overall, H₂¹⁸O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal–bacterial synergies may support bacterial resilience to moisture limitation.Subject terms: DNA sequencing, Fungal ecology, Stable isotope analysis, Climate-change ecology, Microbial ecology     

Microbial Functional Potential and Community Composition in Permafrost-Affected Soils of the NW Canadian Arctic

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic.     

枯草芽胞杆菌菌肥对有机冬瓜根区土壤微生态的影响

【背景】微生物肥料已广泛应用于我国有机作物的种植,其对有机种植土壤微生态的影响尚需科学评测。【目的】高通量测序技术可用于精确分析土壤微生物群落,从细菌、真菌群落结构和多样性的角度阐释枯草芽胞杆菌菌肥对有机农田根区土壤微生物群落的影响。【方法】在有机农田轮作种植条件下,施用枯草芽胞杆菌菌肥后提取冬瓜根区土壤基因组DNA,通过PCR扩增建立文库,利用IlluminaMiSeq高通量测序技术,并结合相关生物信息学方法分析土壤细菌16SrRNA基因V3-V4区和真菌ITS1区的多样性指数及群落结构;测定根区土壤化学性质及酶活性,分析有机冬瓜果实品质,并作相关分析。【结果】从6个有机冬瓜根区土壤样本中获得14199个细菌操作分类单元(OTU)和3378个真菌OTU,细菌和真菌文库测序覆盖率分别在98%、99%以上。枯草芽胞杆菌菌肥会在一定程度上提高土壤细菌种群多样性而降低真菌种群多样性,丰富了细菌群落结构,但显著降低了真菌群落丰富度(P0.05);并减少了根区土壤特有细菌和真菌物种。变形菌门、厚壁菌门和放线菌门是优势细菌,子囊菌门是优势真菌;枯草芽胞杆菌菌肥会提高绿弯菌门和子囊菌门的相对丰度,比例分别为46.23%、10.01%;降低变形菌门和担子菌门的相对丰度,比例分别为11.14%、74.72%。枯草芽胞杆菌菌肥显著降低了土壤pH,显著提高了有机冬瓜果实总氨基酸、可溶性固形物等营养成分含量(P0.05)。【结论】施用枯草芽胞杆菌菌肥改变有机冬瓜根区土壤细菌和真菌的丰富度和多样性,降低了土壤pH,提高了有机冬瓜果实品质。     

Soil microbial community successional patterns during forest ecosystem restoration

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.     

Decline in topsoil microbial quotient, fungal abundance and C utilization efficiency of rice paddies under heavy metal pollution across South China

Agricultural soils have been increasingly subject to heavy metal pollution worldwide. However, the impacts on soil microbial community structure and activity of field soils have been not yet well characterized. Topsoil samples were collected from heavy metal polluted (PS) and their background (BGS) fields of rice paddies in four sites across South China in 2009. Changes with metal pollution relative to the BGS in the size and community structure of soil microorganisms were examined with multiple microbiological assays of biomass carbon (MBC) and nitrogen (MBN) measurement, plate counting of culturable colonies and phospholipids fatty acids (PLFAs) analysis along with denaturing gradient gel electrophoresis (DGGE) profile of 16S rRNA and 18S rRNA gene and real-time PCR assay. In addition, a 7-day lab incubation under constantly 25°C was conducted to further track the changes in metabolic activity. While the decrease under metal pollution in MBC and MBN, as well as in culturable population size, total PLFA contents and DGGE band numbers of bacteria were not significantly and consistently seen, a significant reduction was indeed observed under metal pollution in microbial quotient, in culturable fungal population size and in ratio of fungal to bacterial PLFAs consistently across the sites by an extent ranging from 6% to 74%. Moreover, a consistently significant increase in metabolic quotient was observed by up to 68% under pollution across the sites. These observations supported a shift of microbial community with decline in its abundance, decrease in fungal proportion and thus in C utilization efficiency under pollution in the soils. In addition, ratios of microbial quotient, of fungal to bacterial and qCO(2) are proved better indicative of heavy metal impacts on microbial community structure and activity. The potential effects of these changes on C cycling and CO(2) production in the polluted rice paddies deserve further field studies.     

Dispersal alters soil microbial community response to drought

Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.     

长期施用化肥及秸秆还田对砂姜黑土细菌群落的影响

【目的】在施用化肥的基础上进行秸秆还田是提高砂姜黑土肥力的有效措施,以往的研究只注重秸秆还田对土壤结构、肥力等物理化学性状方面的研究,缺少施肥对砂姜黑土微生物群落影响的研究。本研究以安徽蒙城典型的砂姜黑土为研究对象,以期揭示长期施用化肥和秸秆还田对砂姜黑土细菌群落的影响。【方法】采用454高通量测序对砂姜黑土不同农业施肥措施下的细菌群落进行分析研究,并通过生物信息学的分析方法揭示影响砂姜黑土细菌群落的主要因素。【结果】通过对454高通量测序数据的分析,发现砂姜黑土主要的细菌门类为放线菌、变形菌、酸杆菌、绿弯菌和拟杆菌。长期施用化肥显著提高了砂姜黑土肥力和作物产量,但导致了细菌群落结构的显著变化和多样性的显著降低。秸秆还田有利于土壤肥力的进一步提高,但是并没有缓解长期施用化肥对土壤细菌群落产生的不利影响。分析发现土壤pH的变化是导致土壤细菌群落变异的主要因素。【结论】在施用化肥的基础上进行秸秆还田有利于砂姜黑土肥力的提升,然而并没有缓解由施肥导致的土壤酸化对土壤细菌群落组成和多样性产生的不利影响。这暗示秸秆还田可能并未对砂姜黑土微生物生态产生根本性的有益影响,对于秸秆农田的利用方式还需要进一步研究,以达到农业生产效益和生态效益的并重。     

Diversity and dynamics of microbial communities in soils from agro-ecosystems

Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management.     

Characteristics and diversity of microbial communities in lead–zinc tailings under heavy metal stress in north-west China

High-throughput 16S rRNA and 18S rRNA sequencing were performed to study the changes of soil microbial diversity and community structure under different heavy metal pollution levels in Chengxian lead–zinc mining area, Gansu Province. In this study, we characterized the main physicochemical properties, multiple heavy metal pollution, and microbial community structure of the soil in the tailings. The results show that the soil near the tailings pond was alkaline, barren and the heavy metals were seriously polluted. The microbial diversity and richness of S1 and S2 sites were significantly lower than that of CK2 site (P < 0·05), indicating that the heavy metal pollution could change the physicochemical properties and microbial community structure in soil. Among 97 identified core operating taxa of fungal communities, Ascomycota, Teguta and Basidiomycota were dominant at the phylum level, while among 1523 identified core operating taxa of bacterial communities, Actinomycota was dominant at the phylum level. In addition, the redundancy analysis and Spearman correlation analysis showed that the physicochemical properties and the heavy metal concentration had significant effects on the composition and distribution of soil microbial community. The basic characteristics of soil physicochemical properties, multiple heavy metal pollution and microbial community structure in the tailings were revealed, hoping to provide a basis for ecological rehabilitation of tailings by revealing the variance rule of microbial community diversity in the future.     

Effect of long‐term mineral fertilisation on soil microbial abundance,community structure and diversity in a Typic Hapludoll under intensive farming systems

Fertiliser application can not only influence plant communities, but also the soil microbial community dynamics, and consequently soil quality. Specifically, mineral fertilisation can directly or indirectly affect soil chemical properties, microbial abundance and, the structure and diversity of soil microbial communities. We investigated the impact of six different mineral fertiliser regimes in a maize/soybean rotation system: control (CK, without fertilisation), PS (application of phosphorus plus sulphur), NS (application of nitrogen plus S), NP (application of N plus P), NPS (application of N, P plus S) and NPSm (application of N, P, S plus micronutrients). Soil samples were collected at the physiological maturity stage of maize and soybean in March of 2013 and 2014, respectively. Overall, mineral fertilisation resulted in significantly decreased soil pH and increased total organic carbon compared with the control (CK). The analysis of terminal restriction fragment length polymorphism (T‐RFLP) revealed that mineral fertilisers caused a shift in the composition of both bacterial and fungal communities. In 2013, the highest value of Shannon diversity of bacterial terminal restriction fragments (TRFs) was found in control soils. In 2014, NPSm treated soils showed the lowest values of diversity for both bacterial and fungal TRFs. In both crop growing seasons, the analysis of phospholipid fatty acid (PLFA) detected the lowest value of total microbial biomass under CK. As PLFA analysis can be used to evaluate total microbial community, this result suggests that fertilisation increased total microbial biomass. When the bacterial and fungal abundance were examined using real time polymerase chain reaction, the results revealed that mineral fertilisation led to decreased bacterial abundance (16S rRNA), while fungal abundance (18S rRNA) was found to be increased in both crop growing seasons. Our results show that mineral fertiliser application has a significant impact on soil properties, bacterial and fungal abundance and microbial diversity. However, further studies are needed to better understand the mechanisms involved in the changes to microbial communities as a consequence of mineral fertilisation.     

The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation

The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.     

Soil Bacterial and Fungal Community Structure Across a Range of Unimproved and Semi-Improved Upland Grasslands

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.     

土地利用驱动的土壤性状变化影响微生物群落结构和功能

微生物在调节陆地生态系统地球化学循环过程中具有重要作用。土地利用方式改变显著影响土壤微生物群落结构和功能,但对土地利用驱动的土壤性状变化与微生物群落结构和功能关系的研究相对匮乏。依托长期定位监测试验（始于1984年）,通过16S rRNA基因片段和ITS高通量测序,研究了土地利用方式（裸地、农田、草地）驱动的土壤碳氮变化对微生物群落结构和功能的影响。结果表明：对于细菌群落而言,裸地中α-多样性最高、其次是草地、农田中最低,农田和草地中细菌优势菌群变形菌（Proteobacteria）和放线菌门（Actinobacteria）相对丰度较裸地低4.5%、3.9%和5.5%、3.8%;对于真菌群落而言,裸地子囊菌门（Ascomycota）相对丰度最高、农田次之、草地最低;化能异养型、好氧化能异养型细菌相对丰度裸地显著高于农田和草地（P<0.05）,而硝化型和好氧氨氧化型细菌裸地显著低于农田和草地（P<0.05）;腐生型真菌相对丰度大小排序为：裸地>农田>草地。细菌群落变化主要与土壤容重、全氮、矿质氮、C ： N比和微生物量碳有关,而真菌群落与土壤矿质氮有关。细菌和真菌功能菌群主要受土壤容重、土壤有机碳、土壤全氮、C ： N比和微生物量碳影响。因此,土壤容重、土壤全氮、土壤有机碳、C ： N比、微生物量碳、矿质氮差异可能是影响不同土地利用方式中微生物群落和功能变化的主要因素。     

Differential sensitivity of total and active soil microbial communities to drought and forest management

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning—that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 60 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community‐based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought‐plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.     

Spatial heterogeneity of eukaryotic microbial communities in an unstudied geothermal diatomaceous biological soil crust: Yellowstone National Park, WY, USA

Knowledge of microbial communities and their inherent heterogeneity has dramatically increased with the widespread use of high-throughput sequencing technologies, and we are learning more about the ecological processes that structure microbial communities across a wide range of environments, as well as the relative scales of importance for describing bacterial communities in natural systems. Little work has been carried out to assess fine-scale eukaryotic microbial heterogeneity in soils. Here, we present findings from a bar-coded 18S rRNA survey of the eukaryotic microbial communities in a previously unstudied geothermal diatomaceous biological soil crust in Yellowstone National Park, WY, USA, in which we explicitly compare microbial community heterogeneity at the particle scale within soil cores. Multivariate analysis of community composition showed that while subsamples from within the same soil core clustered together, community dissimilarity between particles in the same core was high. This study describes a novel soil microbial environment and also adds to our growing understanding of microbial heterogeneity and the scales relevant to the study of soil microbial communities.     

Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil

The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h?1 molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium.     

Spatial analysis of a hydrocarbon waste-remediating landfarm demonstrates influence of management practices on bacterial and fungal community structure

Cultivation of dedicated soil plots called ‘landfarms' is an effective technology for bioremediation of hydrocarbon waste generated by various industrial practices. To understand the influence of soil conditions on landfarm microbial communities, analysis of bacterial and fungal community structure using next-generation sequencing at different sections and depths was performed across a hydrocarbon-waste landfarm in Regina, Saskatchewan, Canada. While a core set of hydrocarbon-associated bacterial and fungal taxa are present throughout the landfarm, unique bacterial and fungal operational taxonomic units are differentially abundant at sections within the landfarm, which correlate with differences in soil physiochemical properties and management practices. Increased frequency of waste application resulted in strong positive correlations between bacterial community assemblages and elevated amounts of oil, grease and F3 – F4 hydrocarbon fractions. In areas of standing water and lower application of hydrocarbon, microbial community structure correlated with soil pH, trace nutrients and metals. Overall, diversity and structure of bacterial communities remain relatively stable across the landfarm, while in contrast, fungal community structure appears more responsive to soil oxygen conditions. Results are consistent with the hypothesis that years of bioremediation activity have shaped microbial communities; however, several management practices can be undertaken to increase efficiency of remediation, including the removal of standing water and soil tilling across the landfarm.