In Situ Dynamics of Microbial Communities during Decomposition of Wheat, Rape, and Alfalfa Residues

Microbial communities are of major importance in the decomposition of soil organic matter. However, the identities and dynamics of the populations involved are still poorly documented. We investigated, in an 11-month field experiment, how the initial biochemical quality of crop residues could lead to specific decomposition patterns, linking biochemical changes undergone by the crop residues to the respiration, biomass, and genetic structure of the soil microbial communities. Wheat, alfalfa, and rape residues were incorporated into the 0–15 cm layer of the soil of field plots by tilling. Biochemical changes in the residues occurring during degradation were assessed by near-infrared spectroscopy. Qualitative modifications in the genetic structure of the bacterial communities were determined by bacterial-automated ribosomal intergenic spacer analysis. Bacterial diversity in the three crop residues at early and late stages of decomposition process was further analyzed from a molecular inventory of the 16S rDNA. The decomposition of plant residues in croplands was shown to involve specific biochemical characteristics and microbial community dynamics which were clearly related to the quality of the organic inputs. Decay stage and seasonal shifts occurred by replacement of copiotrophic bacterial groups such as proteobacteria successful on younger residues with those successful on more extensively decayed material such as Actinobacteria. However, relative abundance of proteobacteria depended greatly on the composition of the residues, with a gradient observed from alfalfa to wheat, suggesting that this bacterial group may represent a good indicator of crop residues degradability and modifications during the decomposition process.     

The Effects of Soil Bacterial Community Structure on Decomposition in a Tropical Rain Forest

Soil microorganisms are key drivers of terrestrial biogeochemical cycles, yet it is still unclear how variations in soil microbial community composition influence many ecosystem processes. We investigated how shifts in bacterial community composition and diversity resulting from differences in carbon (C) availability affect organic matter decomposition by conducting an in situ litter manipulation experiment in a tropical rain forest in Costa Rica. We used bar-coded pyrosequencing to characterize soil bacterial community composition in litter manipulation plots and performed a series of laboratory incubations to test the potential functional significance of community shifts on organic matter decomposition. Despite clear effects of the litter manipulation on soil bacterial community composition, the treatments had mixed effects on microbial community function. Distinct communities varied in their ability to decompose a wide range of C compounds, and functional differences were related to both the relative abundance of the two most abundant bacterial sub-phyla (Acidobacteria and Alphaproteobacteria) and to variations in bacterial alpha-diversity. However, distinct communities did not differ in their ability to decompose native dissolved organic matter (DOM) substrates that varied in quality and quantity. Our results show that although resource-driven shifts in soil bacterial community composition have the potential to influence decomposition of specific C substrates, those differences may not translate to differences in DOM decomposition rates in situ. Taken together, our results suggest that soil bacterial communities may be either functionally dissimilar or equivalent during decomposition depending on the nature of the organic matter being decomposed.     

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation.     

Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments

The hyporheic zone of stream ecosystems is a critical habitat for microbial communities. However, the factors influencing hyporheic bacterial communities along spatial and seasonal gradients remain poorly understood. We sought to characterize patterns in bacterial community composition among the sediments of a small stream in southern Ontario, Canada. We used sampling cores to collect monthly hyporheic water and sediment microbial communities in 2006 and 2007. We described bacterial communities terminal-restriction fragment length polymorphism (TRFLP) and tested for spatial and seasonal relationships with physicochemical parameters using multivariate statistics. Overall, the hyporheic zone appears to be a DOC, oxygen, and nitrogen sink. Microbial communities were distinct from those at the streambed surface and from soil collected in the adjacent watershed. In the sediments, microbial communities were distinct between the fall, spring, and summer seasons, and bacterial communities were more diverse at streambed surface and near-surface sites compared with deeper sites. Moreover, bacterial communities were similar between consecutive fall seasons despite shifting throughout the year, suggesting recurring community assemblages associated with season and location in the hyporheic zone. Using canonical correspondence analysis, seasonal patterns in microbial community composition and environmental parameters were correlated in the following way: temperature was related to summer communities; DOC (likely from biofilm and allochthonous inputs) influenced most fall communities; and nitrogen associated strongly with winter and spring communities. Our results also suggest that labile DOC entering the hyporheic zone occurred in concert with shifts in the bacterial community. Generally, seasonal patterns in hyporheic physicochemistry and microbial biodiversity remain largely unexplored. Therefore, we highlight the importance of seasonal and spatial resolution when assessing surface- and groundwater interactions in stream ecosystems.     

Effects of grassland species on decomposition of litter and soil microbial communities

Decomposition of litter is greatly influenced not only by its chemical composition but also by activities of soil decomposers. By using leaf litter from 15 plant species collected from semi-natural and improved grasslands, we examined (1) how interspecific differences in the chemical composition of litter influence the abundance and composition of soil bacterial and fungal communities and (2) how such changes in microbial communities are related to the processes of decomposition. The litter from each species was incubated in soil of a standard composition for 60 days under controlled conditions. After incubation, the structure of bacterial and fungal communities in the soil was examined using phospholipid fatty-acid analysis and denaturing gradient gel electrophoresis. Species from improved grasslands had significantly higher rates of nitrogen mineralization and decomposition than those from semi-natural grasslands because the former were richer in nitrogen. Litter from improved grasslands was also richer in Gram-positive bacteria, whereas that from semi-natural grasslands was richer in actinomycetes and fungi. Nitrogen content of litter also influenced the composition of the fungal community. Changes in the composition of both bacterial and fungal communities were closely related to the rate of litter decomposition. These results suggest that plant species greatly influence litter decomposition not only through influencing the quality of substrate but also through changing the composition of soil microbial communities.     

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition

Plant roots select non‐random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short‐term additions of N, a growth‐limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.     

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil

Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.     

Microbial Colonization of Beech and Spruce Litter—Influence of Decomposition Site and Plant Litter Species on the Diversity of Microbial Community

The present study was conducted to investigate the effect of decomposition site and plant litter species on the colonizing microbial communities. For this, litter bag technique using beech and spruce litter was combined with RNA-based fingerprinting and cloning. Litter bags were incubated for 2 and 8 weeks in the A_h horizon of beech and beech–spruce mixed forest sites. Although sugars and starch were rapidly lost, lignin content increased by more than 40% for beech and more than doubled for spruce litter at both soil sites at the end of the experiment. Denaturing gradient gel electrophoresis analysis of 16S and 18S rRNA RT–PCR products was used for screening of differences between bacterial and fungal communities colonizing the two litter types. Development of the microbial community over time was observed to be specific for each litter type and decomposition site. RT–PCR products from both litter types incubated in beech–spruce mixed forest site were also cloned to identify the bacterial and fungal colonizers. The 16S rRNA clone libraries of beech litter were dominated by γ-proteobacterial members, whereas spruce libraries were mainly composed of α-, β-, and γ-proteobacterial members. Ascomycota members dominated the 18S rRNA clone libraries. Clones similar to Zygomycota were absent from spruce, whereas those similar to Basidiomycota and Glomeromycota were absent from beech libraries. Selective effects of litter quality were observed after 8 weeks. The study provides an insight into the bacterial and fungal communities colonizing beech and spruce litter, and the importance of litter quality and decomposition site as key factors in their development and succession.     

A Coexisting Fungal-Bacterial Community Stabilizes Soil Decomposition Activity in a Microcosm Experiment

How diversity influences the stability of a community function is a major question in ecology. However, only limited empirical investigations of the diversity–stability relationship in soil microbial communities have been undertaken, despite the fundamental role of microbial communities in driving carbon and nutrient cycling in terrestrial ecosystems. In this study, we conducted a microcosm experiment to investigate the relationship between microbial diversity and stability of soil decomposition activities against changes in decomposition substrate quality by manipulating microbial community using selective biocides. We found that soil respiration rates and degradation enzyme activities by a coexisting fungal and bacterial community (a taxonomically diverse community) are more stable against changes in substrate quality (plant leaf materials) than those of a fungi-dominated or a bacteria-dominated community (less diverse community). Flexible changes in the microbial community composition and/or physiological state in the coexisting community against changes in substrate quality, as inferred by the soil lipid profile, may be the mechanism underlying this positive diversity–stability relationship. Our experiment demonstrated that the previously found positive diversity–stability relationship could also be valid in the soil microbial community. Our results also imply that the functional/taxonomic diversity and community ecology of soil microbes should be incorporated into the context of climate–ecosystem feedbacks. Changes in substrate quality, which could be induced by climate change, have impacts on decomposition process and carbon dioxide emission from soils, but such impacts may be attenuated by the functional diversity of soil microbial communities.     

The short-term effects of surface soil disturbance on soil bacterial community structure at an experimental site near Scott Base, Antarctica

Humans are visiting Antarctica in increasing numbers, and the ecological effect of rapid soil habitat alteration due to human-induced physical disturbance is not well understood. An experimental soil disturbance trial was set up near Scott Base on Ross Island, to investigate the immediate and short-term changes to bacterial community structure, following surface soil disturbance. Three blocks, each comprising an undisturbed control, and an area disturbed by removing the top 2 cm of soil, were sampled over a time series (0, 7, 14, 21, and 35 days), to investigate changes to bacterial community structure using DNA profiling by terminal restriction fragment length polymorphism. The simulated disturbance did not cause any major shifts in the structure of the bacterial communities over the 35-day sampling period. Ordination showed that the bacterial community composition correlated strongly with soil EC (R ² = 0.55) and soil pH (R ² = 0.67), rather than the removal of the top 2 cm of surface material. Although the replicate blocks were visually indistinguishable from one another, high local spatial variability of soil chemical properties was found at the study site and different populations of bacterial communities occurred within 2 m of one another, within the same landscape unit. Given the current knowledge of the drivers of bacterial community structure, that is, soil EC, soil pH, and soil moisture content, a follow-up investigation incorporating DNA and RNA-based analyses over a time frame of 2–3 years would lead to a greater understanding of the effects of soil disturbance on bacterial communities.     

沙坡头地区凋落物分解及其对土壤微生物群落的影响

以腾格里沙漠东南缘沙坡头人工固沙植被区典型植物种凋落物(小画眉草、藓类、油蒿叶片)为对象,运用凋落物分解袋法和高通量测序技术,分析了3种植物凋落物分解特征及其对土壤微生物群落的影响。结果表明: 分解时间和凋落物类型均显著影响分解速率,藓类分解最慢,13个月后质量损失比仅为15.4%,油蒿叶片和小画眉草的平均分解速率分别是藓类的4.9和3.4倍。经过11个月的分解,细菌群落的优势菌门为放线菌门和变形菌门,真菌群落的优势菌门是子囊菌门;藓类分解过程中,拟杆菌门和绿弯菌门的相对丰度显著增加,担子菌门的相对丰度显著降低。凋落物分解后,细菌和真菌群落物种多样性和丰富度显著增加,细菌群落组成在凋落物间变化不显著,真菌群落变化显著。凋落物的分解速率与细菌和真菌群落多样性及丰富度均呈负线性变化。植物多糖、全磷和土壤pH、微生物生物量氮、铵态氮含量是影响微生物群落结构的主要因子。凋落物分解改变了土壤微生物群落物种组成和种间相似性,显著增加了土壤中微生物群落的多样性和丰富度,促进了土壤生境的恢复。     

Succession of Bacterial Populations during Plant Residue Decomposition in Rice Field Soil

The incorporation of rice residues into paddy fields strongly enhances methane production and emissions. Although the decomposition processes of plant residues in rice field soil has been documented, the structure and dynamics of the microbial communities involved are poorly understood. The purpose of the present study was to determine the dynamics of short-chain fatty acids and the structure of bacterial communities during residue decomposition in a rice field soil. The soil was anaerobically incubated with the incorporation of rice root or straw residues for 90 days at three temperatures (15, 30, and 45°C). The dynamics of fatty acid intermediates showed an initial cumulative phase followed by a rapid consumption phase and a low-concentration quasi-steady state. Correspondingly, the bacterial populations displayed distinct successions during residue decomposition. Temperature showed a strong effect on the dynamics of bacterial populations. Members of Clostridium (clusters I and III) were most dominant in the incubations, particularly in the early successions. Bacteroidetes and Chlorobi were abundant in the later successions at 15 and 30°C, while Acidobacteria were selected at 45°C. We suggest that the early successional groups are responsible for the decomposition of the easily degradable fraction of residues, while the late successional groups become more important in decomposing the less-degradable or resistant fraction of plant residues. The bacterial succession probably is related to resource availability during residue decomposition. The fast-growing organisms are favored at the beginning, while the slow-growing bacteria are better adapted in the later stages, when substrate availability is limiting.Rice residues, including root and straw residues, serve as the major carbon source in paddy fields. It has been estimated that the amounts of organic matter supplied annually to paddy fields range from 1,700 to 3,470 kg ha⁻¹, and more than 65% of them were derived from plant residues (19, 23). The incorporation of rice residues into paddy fields helps sustain soil organic matter, improve physical and chemical properties, and increase nutrient availability (15, 39). However, it also strongly enhances methane production and emissions (6, 45, 46).Numerous studies have been carried out on residue decomposition and CH₄ production in rice field soils (11-13, 22). The rate of decomposition usually is separated into a fast phase and a slowdown phase (24). According to the dynamics of the intermediates H₂ and fatty acids and the activities of polysaccharolytic enzymes, Glissmann and Conrad (13) proposed five stages for residue decomposition, including the production and consumption of reducing sugars, the production and consumption of H₂ and fatty acids, and the production of CH₄. The rate of decomposition was affected by the composition of residues (11, 18). Root residues generally are decomposed slower than straw residues (24). The fermentation pathway also could differ depending on the residue material, resulting in different fatty acid intermediates (13).A complex microbial assemblage consisting of hydrolytic, fermenting, homoacetogenic, syntrophic, and methanogenic microorganisms are involved in the anaerobic decomposition of organic residues (5, 41, 48). Plant residues are composed of complex components. With the decomposition process, the proportion of labile component decreases while the resistant components relatively accumulate. Changes in the activity and structure of the microbial community thus are anticipated during the processes of residue decomposition. However, little has been known about the dynamics of microbial populations during residue decomposition in anoxic rice soil. Using culture-independent methods, Weber et al. (47) showed that the structure of the bacterial community shifted between early and late stages. Microscopic observation revealed the differential colonizations of bacterial populations on different parts of straw residue, indicating the effects of residue quality and niche condition (18). The microbial community appears to form a spatially well organized architecture, with the fermenting bacteria colonizing the residue particles, while the syntrophic bacteria and methanogens mainly inhabit the adjacent soil during the decomposition process (12).Air temperature exhibits a large seasonal variation in southeastern Asia, where rice is widely cultivated. The lowest and highest records in our research site, for instance, were −5 and 40°C, respectively, in 2006, when we collected the soil samples. It has been demonstrated that temperature has a strong effect on residue decomposition and CH₄ production (8, 22, 33). However, it is uncertain whether the effect also is reflected in the structure and function of degrading microbial communities in the soil. Therefore, the purpose of our project was to determine the effect of temperature on microbial communities during the processes of plant residue decomposition in a Chinese rice field soil. The dynamics of methanogenesis and methanogenic archaea have been reported previously (33). Here, we show the results on fatty acid intermediates and the responsible bacterial communities.     

Soil biota composition and the performance of a noxious weed across its invaded range

The success of invasive plant species is driven, in part, by feedback with soil ecosystems. Yet, how variation in belowground communities across latitudinal gradients affects invader distributions remains poorly understood. To determine the effect of soil communities on the performance of the noxious weed Cirsium arvense across its invaded range, we grew seedlings for 40 days in soils collected across a 699 km linear distance from both inside and outside established populations. We also described the mesofaunal and bacterial communities across all soil samples. We found that C. arvense typically performed better when grown in soils sourced from northern populations than from southern locations where it has a longer invasion history. We also found evidence that C. arvense performed best in soils sourced from outside invaded patches, although this was not consistent across all sites. The bacterial community showed a significant increase in the magnitude of compositional change in invaded sites at higher latitudes, while the mesofaunal community showed the opposite pattern. Bacterial community composition was significantly correlated with C. arvense performance, although mesofaunal community composition was not. Our results demonstrate that the interactions between an invasive plant and associated soil communities change across the invaded range, and the bacterial community in particular may affect variation in plant performance. Observed patterns may be caused by C.arvense presence and time since invasion allowing for an accumulation of species‐specific pathogens in southern soils, while the naïveté of northern soils to invasion results in a more responsive bacterial community. Although these interactions are difficult to predict, such effects could possibly facilitate the establishment of this exotic species to novel locations.     

盐城滨海滩涂湿地典型植物群落土壤微生物组成与结构特征

土壤微生物是生态系统维持正常结构与功能的重要组成部分,为探究盐城滩涂典型湿地土壤微生物群落结构特征,以江苏盐城滩涂互花米草、藨草、盐地碱蓬、芦苇及淤泥质光滩5种典型群落为对象,采用16S rRNA高通量测序技术分析0—10 cm(表层)、10—30 cm(中层)、30—60 cm(深层)土壤微生物多样性及群落结构。结果表明：(1)几种植物群落间,土壤微生物群落结构差异较大,主要体现在细菌群落结构的差异性,古菌群落结构差异相对较小。光滩与植物群落间,在土壤细菌种类及相对丰度上差异相对较大,互花米草群落与本土植物群落间,在微生物群落的细菌种类组成上存在较大差异;藨草群落土壤表层微生物群落结构与互花米草群落相似,深层与盐地碱蓬、芦苇群落相似。(2)同一群落不同层次土壤微生物群落结构相似,差异小于不同群落间土壤微生物群落的结构差异性;不同群落对应层次间,表深层土壤中五种群落土壤微生物多样性存在显著差异,中层土壤中五种群落微生物多样性差异不显著。总体上,植物群落类型对土壤微生物群落结构的影响大于土壤深度;与本土植物群落相比,互花米草群落土壤主要优势门微生物种类差异较小,但部分优势门微生物相对丰度...     

Decomposition of Bt transgenic rice residues and response of soil microbial community in rapeseed–rice cropping system

In this study, Bt transgenic rice (KMD rice) residue decomposition and the associated microbial community in a rapeseed–rice cropping system were assessed in comparison with its parental non-Bt rice variety (XiuShui 11). Decomposition was measured as mass loss by straw and root decay in litterbags over two consecutive years. Bacterial and fungal community compositions associated with residue decomposition were detected by terminal restriction fragment length polymorphism (T-RFLP) and the additive main effects multiplicative interaction (AMMI) analysis model. Decomposition dynamics and bacterial and fungal communities associated with decomposition were strongly affected by surface and incorporated placements, and by temporal factors. However, no significant differences were observed between Bt and non-Bt rice variety in either decomposition dynamics or in the soil microbial communities associated with residue decay. Our field study indicated that the insertion of the cry1Ab gene into Xiushui 11 rice genome had no significant effect on the residual decay and decomposition-associated microbial community compositions in the rapeseed-rice cropping system.     

Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities

Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four ¹³C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the ¹³C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-¹³C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by ¹³C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram + biomarkers showed more incorporation of SOM-C than did Gram – biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More ¹³C (from both simple and recalcitrant sources) was incorporated into the Gram – biomarkers than Gram + biomarkers despite the fact that the Gram + group generally comprised a greater portion of the bacterial biomass than did markers for the Gram – group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles of microbial communities responsible for decomposition of the more recalcitrant substrates, pine litter and indigenous soil organic matter.     

Analysis of Soil Whole- and Inner-Microaggregate Bacterial Communities

Although soil structure largely determines energy flows and the distribution and composition of soil microhabitats, little is known about how microbial community composition is influenced by soil structural characteristics and organic matter compartmentalization dynamics. A UV irradiation-based procedure was developed to specifically isolate inner-microaggregate microbial communities, thus providing the means to analyze these communities in relation to their environment. Whole- and inner-microaggregate fractions of undisturbed soil and soils reclaimed after disturbance by surface coal mining were analyzed using 16S rDNA terminal restriction fragment polymorphism (T-RFLP) and sequence analyses to determine salient bacterial community structural characteristics. We hypothesized that inner-microaggregate environments select for definable microbial communities and that, due to their sequestered environment, inner-microaggregate communities would not be significantly impacted by disturbance. However, T-RFLP analysis indicated distinct differences between bacterial populations of inner-microaggregates of undisturbed and reclaimed soils. While both undisturbed and reclaimed inner-microaggregate bacterial communities were found dominated by Actinobacteria, undisturbed soils contained only Actinobacteridae, while in inner-microaggregates of reclaimed soils Rubrobacteridae predominate. Spatial stratification of division-level lineages within microaggregates was also evidenced, with Proteobacteria clones being prevalent in libraries derived from whole microaggregates. The fractionation methods employed in this study therefore represent a valuable tool for defining relationships between biodiversity and soil structure.     

Minerals Affect the Specific Diversity of Forest Soil Bacterial Communities

Minerals constitute an ecological niche poorly investigated in the soil, in spite of their important role in biogeochemical cycles and plant nutrition. To evaluate the impact of minerals on the structure of the soil bacterial communities, we compared the bacterial diversity on mineral surfaces and in the surrounding soil. Three pure and calibrated minerals (apatite, plagioclase and a mix of phlogopite-quartz) were buried into the organo-mineral layer of a forest soil. After a 4-year incubation in soil conditions, mineral weathering and microbial colonization were evaluated. Apatite and plagioclase were the only two significantly weathered minerals. The analysis of the 16S rRNA gene sequences generated by the cloning-sequencing procedure revealed that bacterial diversity was higher in the surrounding soil and on the unweathered phlogopite-quartz samples compared with the other minerals. Moreover, a multivariate analysis based on the relative abundance of the main taxonomic groups in each compartments of origin demonstrated that the bacterial communities from the bulk soil differed from that colonizing the minerals. A significant correlation was obtained between the dissolution rate of the minerals and the relative abundance of Beta-proteobacteria detected. Notably, many sequences coming from bacteria colonizing the mineral surfaces, whatever the mineral, harbored high similarity with efficient mineral weathering bacteria belonging to Burkholderia and Collimonas genera, previously isolated on the same experimental site. Taken together, the present results provide new highlights concerning the bacterial communities colonizing minerals surfaces in the soil and suggests that the minerals create true ecological niches: the mineralosphere.     

Storage conditions and animal source influence the dominant bacterial community composition in animal manure

The aim of this study was to determine the impact of storage, animal diet, and animal source on the bacterial community composition of manure. The differences among bacterial community structures in fresh manure from cows on two different diets, cow manure stored in a deep pit for about one month, and fresh pig manure were compared. A molecular approach consisting of terminal restriction fragment length polymorphism (T-RFLP), in combination with sequence information from clone libraries, facilitated the identification of specific dominant bacterial populations that varied significantly among manures from different sources and treatments. One such population, represented by TRF 157, the most dominant peak of the bacterial community from stored manure, was identified as a Spirochaeta sp. Interestingly, this peak was absent in the fresh manure communities. The prevailing species in the fresh manure bacterial communities were distinct from those in manure from the storage pit, indicating a major shift in bacterial community composition induced by storage conditions. Moreover, distinct differences in bacterial communities were observed among animal source, but not animal feed. Manure storage is consequently an important parameter to consider when handling fertilizers, in order to obtain an optimal soil microbial ecosystem functioning.