Soil Bacterial Community Profiles Research Articles

The effects of warming and soil chemistry on bacterial community structure in Arctic tundra soils

Soil microbial communities in the Arctic play a critical role in regulating the global carbon (C) cycle. Vast amounts of C are stored in northern high latitude soils, and rising temperatures in the Arctic threaten to thaw permafrost, making relatively inaccessible C sources more available for mineralization by soil microbes. Few studies have characterized how microbial community structure responds to thawing permafrost in the context of varying soil chemistries associated with contrasting tundra landscapes. We subjected active layer and permafrost soils from upland and lowland tundra sites on the North Slope of Alaska to a soil-warming incubation experiment and compared soil bacterial community profiles (obtained by 16S rRNA amplicon sequencing) before and after incubation. The influence of soil composition (characterized by mid-infrared [MIR] spectroscopy) on bacterial community structure and class abundance was analyzed using redundancy and correlation analyses. We found increased abundances of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes [Sphingobacteriia] post incubation, particularly in permafrost soils. The categorical descriptors site and soil layer had the most explanatory power in our predictive models of bacterial community structure, highlighting the close relationship between soil bacteria and the soil environment. Specific soil chemical attributes characterizing the soil environments that were found to be the best predictors included MIR spectral bands associated with inorganic C, silicates, amide II (CN stretch), and carboxylics (C–O stretch), and MIR peak ratios representing C substrate quality. Overall, these results further characterize soil bacterial community shifts that may occur as frozen environments with limited access to C sources, as is found in undisturbed permafrost, transition to warmer and more C-available environments, as is predicted in thawing permafrost due to climate change.

Pyrosequencing reveals profiles of soil bacterial communities after 12 years of conservation management on irrigated crop rotations

Potato and sugar beet, which are widely grown in southern Alberta, may degrade soil quality because they return little C to the soil, and their harvesting methods cause soil disturbance that increases erosion risk. To reverse these effects, a 12-yr study was established to evaluate soil conservation (CONS) management systems for rotations that included potato, sugar beet, dry bean and wheat. These systems, comprising addition of feedlot manure compost, reduced tillage, diverse crop rotations and use of cover crops, were applied to 3- to 5-yr crop rotations. They were compared with conventional (CONV) management systems that did not have any of the CONS practices. In the final year of the study, pyrosequencing was used to determine differences in soil bacterial community profiles between the two systems (CONS vs. CONV) in wheat rhizosphere and bulk soil. Thirteen phyla were observed, and the most abundant were Proteobacteria (39.6%), Actinobacteria (19.1%) and Acidobacteria (14.9%). Soil bacterial α-diversity increased under CONS relative to CONV management. However, whereas the relative abundances of Bacteroidetes and Firmicutes were greater under CONS than CONV management, the reverse was observed for Acidobacteria and Gemmatimonadetes. Proteobacteria were also more abundant under CONS than CONV management, but only in bulk soil. The community structures of the bacterial communities were in agreement with the differences in relative abundances. These differences were consistent with the ecological classification of soil bacteria as copiotrophic or oligotrophic. Therefore, CONS management systems altered the soil bacterial community profiles and increased the productivity of these soils.

Biodegradation of a biochar-modified waterborne polyacrylate membrane coating for controlled-release fertilizer and its effects on soil bacterial community profiles.

Biochar-modified polyacrylate-like polymers are promising waterborne polymer-based membrane coatings for controlled-release fertilizers. However, the effect of these membrane polymers on paddy soil is unknown. A soil incubation experiment was conducted using Fourier transform infrared photoacoustic spectroscopy to monitor the changes in the polymer-coated membranes in paddy soil, and Biolog EcoPlates and polymerase chain reaction-denaturing gradient gel electrophoresis were used to detect the effects of the membranes on soil bacterial community profiles. Compared to unmodified membranes, the biodegradation rate of the biochar-modified membrane was slower, and the membrane was more intact, which improved and guaranteed the controlled release of nutrients. Compared to the soil without membranes, the biochar-modified membranes, as well as unmodified ones, showed no significant impacts on the composition diversity of soil dominant bacterial community. The activity and functional diversity of soil culturable microbial community during the early stage of incubation were reduced by biochar-modified membranes due to the release of small amount of soluble organic materials but were both recovered in the 12(th) month of the incubation period. Therefore, the biochar-modified waterborne polyacrylate was environmentally friendly, demonstrating its potential both in the development of coated controlled-release fertilizers and in the utilization of crop residue.

An RNA-based analysis of changes in biodiversity indices in response to Sus scrofa domesticus decomposition

Despite emergent research initiatives, significant knowledge gaps remain of soil microbiology-associated cadaver decomposition. Nevertheless, preliminary studies have shown that the vast diversity and complex interactions of soil microbial communities have great potential for forensic applications such as clandestine grave location and postmortem interval estimation. This study investigated changes in soil bacterial communities during pig (Sus scrofa domesticus) leg decomposition. 16S rRNA, instead of the usually applied 16S rDNA marker, was used to compare the metabolically active bacteria. Total bacterial RNA was extracted from soil samples of three different layers on day 3, 28 and 77 after the shallow burial of a pig leg. The V3 region of the 16S rRNA was amplified, analysed by RT-PCR DGGE, and compared with control soil bacterial community profiles. Statistically significant differences in soil bacterial biodiversity were observed. For the control, bacterial diversity (H′) and species richness (S) of the three layers averaged 2.48±0.14 (H′) and 18.8±2.5 (S), respectively, while for the test soil increases (p=0.027) were recorded between day 3 (H′=2.71±0.02; S=21.3±2.0) and 28 (H′=3.46±0.32; S=60.3±16.9), particularly in the middle (10–20cm) and bottom (20–30cm) soil layers. Between day 28 and 77 the diversity and richness then decreased on average for all three layers (H′=3.43±0.20; S=60.0±17.3) but remained higher than on day 3. Thus, responses in soil bacterial profiles and activity to carcass decomposition, detected and characterised by RNA-based DGGE, could be used together with RNA sequencing data, changes in physico-chemical variables (carbon, nitrogen, phosphorus, temperature, redox potential, water activity and pH) and conventional macroecology markers (e.g. insects and vegetation), to develop a suite of analytical protocols for different forensic scenarios.

Use of mycelia as paths for the isolation of contaminant‐degrading bacteria from soil

SummaryMycelia of fungi and soil oomycetes have recently been found to act as effective paths boosting bacterial mobility and bioaccessibility of contaminants in vadose environments. In this study, we demonstrate that mycelia can be used for targeted separation and isolation of contaminant‐degrading bacteria from soil. In a ‘proof of concept’ study we developed a novel approach to isolate bacteria from contaminated soil using mycelia of the soil oomycete Pythium ultimum as translocation networks for bacteria and the polycyclic aromatic hydrocarbon naphthalene (NAPH) as selective carbon source. NAPH‐degrading bacterial isolates were affiliated with the genera Xanthomonas, Rhodococcus and Pseudomonas. Except for Rhodococcus the NAPH‐degrading isolates exhibited significant motility as observed in standard swarming and swimming motility assays. All steps of the isolation procedures were followed by cultivation‐independent terminal 16S rRNA gene terminal fragment length polymorphism (T‐RFLP) analysis. Interestingly, a high similarity (63%) between both the cultivable NAPH‐degrading migrant and the cultivable parent soil bacterial community profiles was observed. This suggests that mycelial networks generally confer mobility to native, contaminant‐degrading soil bacteria. Targeted, mycelia‐based dispersal hence may have high potential for the isolation of bacteria with biotechnologically useful properties.

The bacterial biogeography of British soils

Despite recognition of the importance of soil bacteria to terrestrial ecosystem functioning there is little consensus on the factors regulating belowground biodiversity. Here we present a multi-scale spatial assessment of soil bacterial community profiles across Great Britain (> 1000 soil cores), and show the first landscape scale map of bacterial distributions across a nation. Bacterial diversity and community dissimilarities, assessed using terminal restriction fragment length polymorphism, were most strongly related to soil pH providing a large-scale confirmation of the role of pH in structuring bacterial taxa. However, while α diversity was positively related to pH, the converse was true for β diversity (between sample variance in α diversity). β diversity was found to be greatest in acidic soils, corresponding with greater environmental heterogeneity. Analyses of clone libraries revealed the pH effects were predominantly manifest at the level of broad bacterial taxonomic groups, with acidic soils being dominated by few taxa (notably the group 1 Acidobacteria and Alphaproteobacteria). We also noted significant correlations between bacterial communities and most other measured environmental variables (soil chemistry, aboveground features and climatic variables), together with significant spatial correlations at close distances. In particular, bacterial and plant communities were closely related signifying no strong evidence that soil bacteria are driven by different ecological processes to those governing higher organisms. We conclude that broad scale surveys are useful in identifying distinct soil biomes comprising reproducible communities of dominant taxa. Together these results provide a baseline ecological framework with which to pursue future research on both soil microbial function, and more explicit biome based assessments of the local ecological drivers of bacterial biodiversity.

Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities.

Soil microorganisms drive critical functions in plant-soil systems. As such, various microbial properties have been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts of Zn and/or Cd pollution and Thlaspi caerulescens growth on key soil microbial properties: basal respiration; substrate-induced respiration (SIR); bacterial community structure as assessed by PCR-denaturing gradient gel electrophoresis (DGGE); community sizes of total bacteria, ammonia-oxidizing bacteria, and chitin-degrading bacteria as assessed by quantitative PCR (Q-PCR); and functional gene distributions as determined by functional gene arrays (GeoChip). T. caerulescens proved to be suitable for Zn and Cd phytoextraction: shoots accumulated up to 8,211 and 1,763 mg kg(-1) (dry weight [DW]) of Zn and Cd, respectively. In general, Zn pollution led to decreased levels of basal respiration and ammonia-oxidizing bacteria, while T. caerulescens growth increased the values of substrate-induced respiration (SIR) and total bacteria. In soils polluted with 1,000 mg Zn kg(-1) and 250 mg Cd kg(-1) (DW), soil bacterial community profiles and the distribution of microbial functional genes were most affected by the presence of metals. Metal-polluted and planted soils had the highest percentage of unique genes detected via the GeoChip (35%). It was possible to track microbial responses to planting with T. caerulescens and to gain insight into the effects of metal pollution on soilborne microbial communities.

Antibiotic resistance profiles of soil bacterial communities over a land degradation gradient

This study profiled soils over a land degradation gradient to obtain formulae as integrative measures for describing the gradient as a result of deforestation in Thailand. We applied antibiotic resistance most-probable-number profiling to the soil bacterial communities, and then described the gradient. Soil samples were collected on the gradient represented by dry evergreen forest (the original vegetation), dry deciduous forest (moderately disturbed) and bare ground (the most degraded) in February (dry season), March (shortly after temporal precipitation) and June (rainy season) 2001. In the period of this study, the degradation was consistently shown as soil conditions like sandy texture, high bulk density, lower pH, high exchangeable acidity, poor mineral and organic nutrients and dryness. Soil fertility index and soil evaluation factor, as the integrative measures of the intensity of land degradation, were described by scores on the first or the second principal component derived from the soil bacterial community profiles for each sampling time (R>0.457, p 0.501, p<0.001), suggesting great dry to moist seasonal effects. Further, the changes had significant relationships with gradients of soil moisture content, acidity and/or soil nitrogen content. The data sets on the soil bacterial community profiles had more complicated data structures than the physicochemical data sets, suggesting effects of the physicochemical changes on the soil bacterial community. The differences between the bacterial and the physicochemical aspects suggest that it is advantageous to observe multiple aspects of soil quality when describing a soil-related gradient of interest.

Soil bacterial community structure and physicochemical properties in mitigation wetlands created in the Piedmont region of Virginia (USA)

Wetland creation is a common practice for compensatory mitigation in the United States. Vegetation attributes have been used as a quick measure of mitigation success in most post-creation monitoring, while little attention has been paid to soils that provide the substrate for flora and fauna to establish and develop. Created wetland soils are often found not indicative of ‘hydric soil’ with a lack of development of physicochemical properties (i.e., bulk density, moisture content, and carbon and nitrogen contents) comparable to those in natural wetlands. Moreover, soil bacterial communities are rarely examined though they are integrally involved in biogeochemical functions that are critical for ecosystem development in created wetlands. We analyzed soil physicochemistry and profiled soil bacterial community structure using amplicon length heterogeneity polymerase chain reaction (LH-PCR) of 16S ribosomal DNA in three relatively young wetlands (<10 years old) created in the Piedmont region of Virginia. We examined the data by site and by specific conditions of each site (i.e., induced microtopography and hydrologic regime). Multidimensional scaling (MDS) and analysis of similarity (ANOSIM) showed clear clustering and significant differences both in soil physicochemistry (Global R = 0.70, p = 0.001) and in soil bacterial community profiles (Global R = 0. 77, p = 0.001) between sites. Soil physicochemistry (Global R = 1, p = 0.005) and bacterial community structure (Global R = 0.79, p = 0.005) of soils significantly differed by hydrologic regime within a wetland, but not by microtopography treatment. A significant association was found between physicochemistry and bacterial community structure in wetland soils, revealing a close link between two attributes ( ρ = 0.39, p = 0.002) . C/N (carbon to nitrogen) ratio was the best predictor of soil bacterial community patterns ( ρ = 0.56, p = 0.001). The diversity of soil bacterial community (Shannon's H′) differed between sites with a slightly higher diversity observed in a relatively older created wetland, and seemed also fairly determined by hydrologic regime of a site, with a relatively dry site being more diverse.

Community-level physiological profiling in monitoring rehabilitative effects of Acacia auriculiformis plantation on degraded land in Sakaerat, Thailand

This study was conducted to investigate the rehabilitative effects of planting Acacia auriculiformis trees on degraded land by observing variations in soil bacterial community profiles provided by community-level physiological profiling. Soil bacterial and physicochemical comparisons between an original evergreen forest and the Acacia plantation plot, established on an area severely degraded as a result of deforestation, showed that most soil characteristics were rehabilitated 18 to 19 years after the plantation of Acacia according to single variables, Shannon and Simpson diversity indices based on the community-level physiological profiles, principal component analysis and redundancy analysis. However, a more strict statistical comparison, discriminant analysis, completely discriminated between the Acacia plantation and the evergreen forest soils when the community-level physiological profiles were compared. Thus, the Acacia plantation soil was shown to still be in the process to full recovery. Here, we discuss the relevance of planting A. auriculiformis in land rehabilitation schemes in savanna regions.