Eubacterial communities in different soil macroaggregate environments and cropping systems

Different positions within soil macroaggregates, and macroaggregates of different sizes, have different chemical and physical properties which could affect microbial growth and interactions among taxa. The hypothesis that these soil aggregate fractions contain different eubacterial communities was tested using terminal restriction fragment length polymorphism (T-RFLP) of the 16S ribosomal gene. Communities were characterized from two field experiments, located at the Kellogg Biological Station (KBS), MI, USA and the Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA. Three soil management regimes at each site were sampled and management was found to significantly affect T-RFLP profiles. The soil aggregate erosion (SAE) method was used to isolate aggregate regions (external and internal regions). Differences between eubacterial T-RFLP profiles of aggregate exteriors and interiors were marginally significant at KBS (accounting for 12.5% of total profile variance), and not significant at OARDC. There were no significant differences among macroaggregate size classes at either site. These results are in general agreement with previous studies using molecular methods to examine microbial communities among different soil macroaggregate size fractions, although further study of communities within different aggregate regions is warranted. Analysis of individual macroaggregates revealed large inter-aggregate variability in community structure. Hence the tertiary components of soil structure, e.g. arrangement of aggregates in relation to shoot residue, roots, macropores, etc., may be more important than aggregate size or intra-aggregate regions in the determination of the types of microbial communities present in aggregates. Direct microscopic counts were also used to examine the bacterial population size in aggregate regions at KBS. The proportion of bacterial cells with biovolumes >0.18 μm³ was higher in aggregate interiors than in exteriors, indicating potentially higher activity in that environment. This proportion was significantly related to percent C of the samples, while total bacterial cell counts were not.     

Physiological and molecular characterisation of microbial communities associated with different water-stable aggregate size classes

We determined if the structure and function of microbial communities associated with different aggregate size classes was influenced when the aggregate formation occurred under either nitrogen (N) limitation (straw only incubation treatment) or carbon (C) limitation (straw+N incubation treatment). Using a combination of community-level physiological (BD Oxygen Biosensor assay) and molecular (terminal restriction fragment length polymorphism; T-RFLP) profiling methods, we found differences in both microbial community composition and the physiological response of these communities between different aggregate size classes. The response of fungal and bacterial communities to ‘straw only’ and ‘straw+N’ treatments differed in that bacterial community composition was affected by the treatments, whereas fungal community composition was not. The magnitude of change in the bacterial community response increased with decreasing aggregate size. However, there were no significant differences in the mean bacterial community richness (number of different terminal restriction fragments; TRFs) between different aggregate size classes for the two treatments. In general, microbial communities associated with larger aggregate size fractions (large and small macroaggregates) were found to have a significantly faster respiratory response than the communities associated with microaggregates. Application of the fungal inhibitor cycloheximide resulted in a significant reduction in the utilization of cellulose, chitin, mannose, xylan, and xylose by the microbial communities associated with all aggregate size classes, indicating that fungi are significant contributors to the utilization of these compounds. Our results demonstrate that the BD Oxygen Biosensor assay offers a valuable new tool for community level physiological profiling. When used in combination with census-based methods such as T-RFLP, a greater level of resolution can be achieved.     

Contributions of soil biota to C sequestration varied with aggregate fractions under different tillage systems

It is increasingly believed that substantial soil organic carbon (SOC) can be sequestered in conservation tillage system by manipulating the functional groups of soil biota. Soil aggregates of different size provide diverse microhabitats for soil biota and consequently influence C sequestration. Our objective was to evaluate the contributions of soil biota induced by tillage systems to C sequestration among different aggregate size fractions. Soil microbial and nematode communities were examined within four aggregate fractions: large macroaggregates (>2 mm), macroaggregates (2–1 mm), small macroaggregates (1–0.25 mm) and microaggregates (<0.25 mm) isolated from three tillage systems: no tillage (NT), ridge tillage (RT) and conventional tillage (CT) in Northeast China. Soil microbial and nematode communities varied across both tillage systems and aggregate fractions. The activity and abundance of microbes and nematodes were generally higher under NT and RT than under CT. Among the four aggregate fractions, soil microbial biomass and diversity were higher in microaggregates, while soil nematode abundance and diversity were higher in large macroaggregates. Structural equation modelling (SEM) revealed that the linkage between microbial and nematode communities and their contributions to soil C accumulation in >1 mm aggregate fractions were different from those in <1 mm aggregate fractions. Higher abundance of arbuscular mycorrhizal fungi (AMF) could enhance C retention within >1 mm aggregates, while more gram-positive bacteria and plant-parasitic nematodes might increase C accumulation within <1 mm aggregates. Our findings suggested that the increase in microbial biomass and nematode abundance and the alteration in their community composition at the micro-niche within aggregates could contribute to the higher C sequestration in conservation tillage systems (NT and RT).     

Effects of the introduction of a biocontrol strain of Trichoderma atroviride on non target soil micro-organisms

The main objective of this study was to assess the impact of the application of an antagonistic strain of Trichoderma atroviride on the native microbial soil communities. The structures of the fungal and bacterial communities were assessed by T-RFLP (terminal restriction fragment length polymorphism) method, based on T-RFLP analysis of 18S and 16S rRNA genes, respectively. Results showed that the introduction of the strain I-1237 into two soils slightly modified the microbial diversity, only for a short period of time. Nine months post-inoculation resilience took place, resulting in similar structures of the fungal and bacterial communities in the inoculated and control soils.     

The distribution of nematodes and soil microbial communities across soil aggregate fractions and farm management systems

We hypothesized that nematode and microbial communities vary between soil aggregate fractions due to variations in physical and/or resource constraints associated with each fraction and that this, in turn, contributes to management impacts on whole soil food webs. Nematode and microbial communities were examined within three soil fractions: large macroaggregates (LM; >1000 μm), small macroaggregates (SM; 250-1000 μm) and inter-aggregate soil and space (IS; <250 μm) isolated from soils of four agricultural management systems: conventional tomato (CON), organic tomato (ORG), a minimum till grain-legume intercrop with continuous cover (CC) and an unmanaged riparian corridor (RC). Aggregate fractions appeared to influence nematode assemblages more than did management system. In general the IS and LM fractions contained higher densities of all nematode trophic groups than did SM. Management × fraction interactions for bacterivores and fungivores, however; suggested a non uniform trend across management systems. The IS fraction exhibited stronger trophic links, per the nematode structure index (SI), while the LM and SM fractions had more active fungal decomposition channels as indicated by the channel index (CI). Higher adult to juvenile ratios in the LM and IS than the SM fraction, and a positive correlation between nematode density in the IS fraction and the proportion of macroaggregates in the soil, indicated an association between soil structure and nematode distribution. Microbial communities varied across both aggregate fractions and management systems. Phospholipid fatty acid (PLFA) analysis suggested that the LM fraction contained greater microbial biomass, gram positive bacteria, and eukaryotes than the IS fraction, while SM contained intermediate PLFA associated with these groups. Total PLFA was greater under RC and ORG than under CC or CON. Total PLFA was positively correlated with % C in soil fractions while nematode abundance exhibited no such relationship. Our findings suggest that microbial communities are more limited by resource availability than by habitable pore space or predation, while nematode communities, although clearly resource-dependent, are better associated with habitable pore space for the soil fractions studied here.     

Development of pollution-induced community tolerance is linked to structural and functional resilience of a soil bacterial community following a five-year field exposure to copper

Copper (Cu) is accumulating in agricultural soils worldwide creating concern for adverse impacts on soil microbial communities and associated ecosystem services. In order to evaluate the structural and functional resilience of soil microbial communities to increasing Cu levels, we compared a Cu-adapted and a corresponding non-adapted soil microbial community for their abilities to resist experimental Cu pollution. Laboratory soil microcosms were set-up with either High-Cu soil from Cu-amended field plots (63 g Cu m⁻²) or with Low-Cu control soil from the same five-year field experiment. Laboratory treatments consisted of Cu amendments in the presence or absence of pig manure. Microbial activities (soil respiration, substrate-induced respiration, [³H]leucine incorporation), bacterial community structure (terminal restriction fragment length polymorphism, T-RFLP), community-level physiological profiles, and pollution-induced bacterial community tolerance (PICT detected using the [³H]leucine incorporation technique) were monitored for 12 weeks. The High-Cu and Low-Cu soil microbial communities initially exhibited almost identical structure and function and could only be distinguished from each other by their differential Cu tolerance. Experimental Cu pollution inhibited microbial activities, affected bacterial community structure, and induced further bacterial community tolerance to Cu. However, Low-Cu and High-Cu soil microbial communities showed essentially identical responses. Manure amendment did not protect against Cu toxicity and slightly increased Cu bioavailability as measured by a Cu-specific whole-cell bacterial biosensor. Our results indicate convergence of bacterial community structure and function in the High-Cu and Low-Cu soils during the five-year field experiment. We conclude that soil bacterial communities can exhibit structural and functional resilience to a five-year Cu exposure by virtue of their ability to develop Cu tolerance without affecting overall community structure. The observed increased Cu tolerance may involve phenotypic adaptation or selection at the micro-diversity level, for example an increased proportion of Cu-resistant strains within each bacterial species, which go undetected by T-RFLP community fingerprinting. Finally, our results indicate that Cu-dissolved organic matter complexes contribute to microbial toxicity in manure-amended soils implying that free Cu may comprise a poor predictor of metal toxicity.     

应用T-RFLP技术分析不同土壤温度和施肥方式下设施土壤细菌群落结构

采用末端限制性片段长度多态性分析(T-RFLP)和荧光定量PCR技术,研究了两种土壤温度(对照不增温,10℃±2℃;增温,20℃±2℃)和两种施肥方式(对照不施肥;鸡粪有机肥底肥+尿素追肥)对土壤细菌群落结构及其多样性和数量特征的影响。结果表明:相同施肥方式下,土壤增温增加土壤速效养分含量,尤其在施肥时增加幅度更明显。分析显示施肥对土壤细菌群落结构的影响在不同土壤温度条件下表现不同。土壤不增温条件下,施肥增加细菌Pielou均匀度指数和Shannon-Weiner多样性指数,Simpson优势度指数降低;土壤增温条件下,则效果相反。与不增温比,增温使土壤细菌Pielou均匀度指数和Shannon-Weiner多样性指数降低,但物种个体数和Simpson优势度指数增加明显。增温改变了土壤细菌群落结构,62 bp和93 bp两种限制性末端片段在土壤增温条件下优势度提高,主要包括共生菌和杆菌。     

A cross-seasonal comparison of active and total bacterial community composition in Arctic tundra soil using bromodeoxyuridine labeling

Arctic soil microorganisms remain active at ecologically relevant rates in frozen soils. We used bromodeoxyuridine (BrdU) labeling and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA gene amplicons to examine active bacterial communities in two Alaskan tundra soils collected in summer and winter of 2005. Active community T-RFLP profiles were compared to total community profiles to determine if active bacteria were a subset of the total community. In shrub soils, active bacteria communities differed in composition between summer and winter, and winter-active bacterial taxa were not detected in the total community, suggesting that they are likely rare within the overall community. In contrast, tussock tundra soil contained more bacterial taxa that were active in both summer and winter and also represented a large portion of the total community. Using in silico digest of a sequence library from this site, we attempted to identify the dominant organisms in our samples. Our previous research suggested that the total microbial community was stable throughout the year, but this new study suggests that the active community is more dynamic seasonally. In general, only a subset of the total community was growing at a given time. This temporal niche partitioning may contribute to the high diversity of microbial communities in soils. Understanding which taxa contribute to microbial function under different conditions is the next frontier in microbial ecology and linking composition to biogeochemical cycling.     

Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled from the Ljubljana Marsh under different seasonal conditions. Substrate-induced respiration and dehydrogenase activity were used as indicators of total microbial activity. Both methods indicated higher microbial activities in the fen soil with the higher SOC content on all dates of sampling. To determine whether the differences in microbial activity were associated with differences in the microbial community structures, terminal restriction fragment length polymorphism (T-RFLP) of bacterial 16S rRNA genes was performed. Comparison of the T-RFLP profiles revealed very similar community structures in both fens and in the two seasonal extremes investigated. This suggested a stable community structure in the two fens, which is not affected by the SOC content or seasonal variation. In addition, a bacterial 16S ribosomal RNA gene based clone library was prepared from the fen soil with the higher SOC content. Out of 114 clones analysed, approximately 53% belonged to the Proteobacteria, 23% to the Acidobacteria, 21% to a variety of other taxa, and less than 3% were affiliated with the Firmicutes.     

Variation of intra‐aggregate organic carbon affects aggregate formation and stability during organic manure fertilization in a fluvo‐aquic soil

The aggregate formation and stability are controlled by the dynamics of soil organic matters (SOM), but how it is related to SOM chemical composition within different‐sized aggregates is largely unknown during manure fertilization. In this study, the variations of intra‐aggregate organic carbon (OC), including intra‐particulate organic matter (iPOM) and mineral‐associated organic matter, were quantitatively and qualitatively analysed, and then, their effects on aggregate formation and stability were assessed under four treatments: control (CK), mineral fertilizer (NPK), reduced manure (30%M) and manure fertilizers (M). Manure application (M) significantly increased macroaggregate proportion, mean weight diameter (MWD), and OC contents within different‐sized aggregates compared to CK, NPK, and 30%M. The OC accumulation of macroaggregate in M was attributed to OC content increase in silt plus clay subfraction rather than iPOM with more labile organic groups; oppositely, in microaggregate it was located in the relatively stable fine iPOM. The macroaggregate formation and stability were controlled by the fine iPOM within macroaggregates, whose abundant polysaccharide‐C and aliphatic‐C after manure fertilization advanced the microbial growth except for Gram‐positive bacteria, which further promoted macroaggregate formation and stability. The free silt plus clay fraction also affected macroaggregate formation and stability, and its polysaccharide‐C derived from microorganisms or decomposing SOM was positively associated with MWD and macroaggregate proportion. Because polysaccharide‐C can be easily associated with mineral particles, further improving micro‐ or macroaggregation. We conclude that continuous manure fertilization could increase labile SOM accumulation within aggregates and then facilitate microbial growth, which collectively are responsible for aggregate formation and stabilization.     

Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems

The hypothesis that soil light fraction and heavy fraction harbor distinct eubacterial communities and have differing numbers and sizes of bacterial cells was tested in three agronomic cropping systems. This hypothesis would imply that these soil fractions are distinct microbial habitats. Shoot residue and rhizosphere soil were also included in the analysis. Terminal restriction fragment length polymorphism (T-RFLP) of 16S ribosomal DNA was used to assay eubacterial community structure. T-RFLP profiles were affected by both soil fraction and cropping system, accounting for 35-50% of the variance in the profiles. T-RFLP profiles separated samples into two distinct eubacterial habitats: soil heavy fraction, which includes the mineral particles and associated humified organic matter, and soil light fraction/shoot residue and rhizosphere, which includes particulate soil organic matter. Differences were not based on organic C content of fractions alone; T-RFLP profiles were also differentiated by cropping system and by rhizosphere versus light fraction/shoot residue. Heavy fraction communities had the least amount of random variability in T-RFLP profiles, resulting in the clearest cropping system effects, while rhizosphere and shoot residue communities were the most variable. Profiles from organically managed corn soil were more variable than for either conventionally managed corn or alfalfa. The log number of bacterial cells per gram fraction was affected by soil fraction but not cropping system, being highest in the light fraction. The percentage of cells >0.18 μm³ was also greater in the light fraction than in other fractions. While bacterial cell density was generally correlated with C content of the soil fraction, heavy fraction did have a significantly greater number of cells per μg C than other soil fractions. The results show that habitat diversity in soil, related both to the amounts and types of organic matter, as well as other potential factors, are important in maintaining the high soil bacterial species diversity and evenness that is found in soil.     

Two-year field study shows little evidence that PPO-transgenic rice affects the structure of soil microbial communities

There is global concern about the environmental consequences associated with transgenic crops. Their effects on the soil ecosystem are of special interest when assessing ecological safety and integrity. Although many efforts have been made to develop crops genetically modified to have resistance to protoporphyrin oxidase (PPO)-inhibiting herbicides, little is known about their influence on soil microbial communities. We conducted a 2-year field study and an analysis via terminal restriction fragment length polymorphism (T-RFLP) to assess the impacts of PPO-transgenic rice on bacterial and fungal communities. In the first year we sampled the rhizosphere and surrounding bulk soil, while in the second year we sampled rhizosphere soil only. No differences were observed in the diversity indices and community composition of microbial communities between transgenic rice and its parental non-transgenic counterpart (cultivar Dongjin). Instead, community variation was strongly dependent on growth stage and year. Therefore, we observed no adverse effects by these crops of modified rice on the microbial community composition in paddy soils.     

转Bt基因棉花根际细菌与古菌群落结构分析

在一年内棉花的四个生长时期（苗期,蕾期,花铃期,吐絮期）分别采集转Bt基因抗虫棉GK12和非转基因亲本棉花泗棉3号根际土壤,以及未种植棉花的背景土壤,利用末端标记限制性片段长度多态性（T-RFLP）分析技术,分析三种土壤中细菌和古菌的16S rRNA基因片段多态性,结合克隆文库建立和测序,研究了土壤中细菌和古菌群落结构的变化.结果表明：在棉花生长的各个时期,背景土壤中细菌群落结构发生了明显的变化,生物多样性指数明显降低,古菌群落结构也有一定的变化,说明季节性变化对土壤中微生物群落产生了明显的影响.与背景土壤相比,棉花种植后根际土壤中细菌和古菌群落发生显著的变化.转基因棉花与非转基因棉花相比,根际土壤细菌和古菌的种类和种群大小的分布也发生了明显的改变.克隆文库和测序结果表明土壤中主体微生物为目前未培养的、功能特性未知的细菌和古菌,转基因棉花种植对这些细菌和古菌影响的原因、环境危害和生态风险目前尚不清楚.与古菌群落相比,棉花种植对细菌群落结构的影响较小.     

Evaluating the physical capture method of terminal restriction fragment length polymorphism for comparison of soil microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) is a popular method of comparative microbial community analysis which is normally accomplished by tagging terminal restriction fragments (T-RFs) with a fluorescent primer. Here, we evaluate an alternative method of T-RFLP where T-RFs are physically captured using a biotinylated primer and streptavidin-coated beads. This eliminates one of the primary criticisms of T-RFLP, namely that T-RFs cannot be identified by sequence analysis, and also represents an alternative method for collecting T-RFLP profiles. Microbial communities from forest, agricultural, and turf soils were investigated using several sets of primers specific for different microbial groups. The physical capture method of T-RFLP resulted in similar profiles to those generated by fluorescent T-RFLP. The relationships among ecosystem types captured by both methods and revealed by ordination were virtually identical. The total variance in the profiles that was attributed to ecosystem type was approximately equal, or greater, when generated by the physical capture method, depending on the primers used. However, physical capture T-RFLP resolved fewer T-RFs than fluorescent T-RFLP, and this may reduce the sensitivity to changes in non-dominant populations within the community. Direct cloning and sequencing of physical capture T-RFs revealed that most bands were not comprised of sequences related to those in the database that would generate T-RFs of similar size. T-RFs should therefore be identified by sequencing, rather than by comparing the sizes of T-RFs to computer digests of database sequences. Physical capture T-RFLP should be a useful tool to identify T-RFs by sequencing, and for laboratories without economical access to equipment required to perform fluorescent T-RFLP.     

Influence of dry–wet cycles on the interrelationship between aggregate,particulate organic matter,and microbial community dynamics

Aggregate dynamics and their relationship to the microbial community have been suggested as key factors controlling SOM dynamics. Dry–wet (DW) cycles are thought to enhance aggregate turnover and decomposition of soil organic matter (SOM), particularly in tilled soils. The objective of this study was to evaluate the effects of DW cycles on aggregate stability, SOM dynamics, and fungal and bacterial populations in a Weld silt loam soil (Aridic Paleustoll). Samples, taken from 250 μm sieved air-dried soil (i.e. free of macroaggregates > 250 μm), were incubated with ¹³C-labeled wheat residue. In one set of soil samples, fungal growth was suppressed using a fungicide (Captan) in order to discern the effect of dry–wet cycles on fungal and bacterial populations. Aggregate formation was followed during the first 14 d of incubation. After this period, one set of soil samples was subjected to four DW cycles, whereas another set, as a control, was kept at field capacity (FC). Over 74 d, total and wheat-derived respiration, size distribution of water stable aggregates and fungal and bacterial biomass were measured. We determined native and labeled C dynamics of three particulate organic matter (POM) fractions related to soil structure: the free light fraction (LF), and the coarse (250–2000 μm) and fine (53–250 μm) intra-aggregate POM fraction (iPOM). In the fungicide treated soil samples, fungal growth was significantly reduced and no large macroaggregates (> 2 mm) were formed, whereas without addition of fungicide, fungi represented the largest part of the microbial biomass (66%) and 30% of the soil dry weight was composed of large macroaggregates. During macroaggregate formation, labeled free LF-C significantly decreased whereas labeled coarse iPOM-C increased, indicating that macroggregates are formed around fresh wheat residue (free LF), which is consequently incorporated and becomes coarse iPOM. The first drying and wetting event reduced the amount of large macroaggregates from 30 to 21% of the total soil weight. However, macroaggregates became slake-resistant after two dry-wet cycles. Fine iPOM-C was significantly lower in soil after two dry–wet cycles compared to soil kept at FC. We conclude that more coarse iPOM is decomposed into fine iPOM in macroaggregates not exposed to DW cycles due to a slower macroaggregate turnover. In addition, when macroaggregates, subjected to dry–wet cycles, became slake-resistant (d 44) and consequently macroaggregate turnover decreased, fine iPOM accumulated. In conclusion, differences in fine iPOM accumulation in DW vs. control macroaggregates are attributed to differences in macroaggregate turnover.     

Rate of soil‐aggregate formation under different organic matter amendments—a short‐term incubation experiment

To improve soil structure and take advantage of several accompanying ecological benefits, it is necessary to understand the underlying processes of aggregate dynamics in soils. Our objective was to quantify macroaggregate (> 250 μm) rebuilding in soils from loess (Haplic Luvisol) with different initial soil organic C (SOC) contents and different amendments of organic matter (OM) in a short term incubation experiment. Two soils differing in C content and sampled at 0–5 and 5–25 cm soil depths were incubated after macroaggregate destruction. The following treatments were applied: (1) control (without any addition), (2) OM₁ (addition of OM: preincubated wheat straw [< 10 mm, C : N 40.6] at a rate of 4.1 g C [kg soil]^–1), and (3) OM₂ (same as (2) at a rate of 8.2 g C [kg soil]^–1). Evolution of CO₂ released from the treatments was measured continuously, and contents of different water‐stable aggregate‐size classes (> 250 μm, 250–53 μm, < 53 μm), microbial biomass, and ergosterol were determined after 7 and 28 d of incubation. Highest microbial activity was observed in the first 3 d after the OM application. With one exception, > 50% of the rebuilt macroaggregates were formed within the first 7 d after rewetting and addition of OM. However, the amount of organic C within the new macroaggregates was ≈ 2‐ to 3‐fold higher than in the original soil. The process of aggregate formation was still proceeding after 7 d of incubation, however at a lower rate. Contents of organic C within macroaggregates were decreased markedly after 28 d of incubation in the OM₁ and OM₂ treatments, suggesting that the microbial biomass (bacteria and fungi) used organic C within the newly built macroaggregates. Overall, the results confirmed for all treatments that macroaggregate formation is a rapid process and highly connected with the amount of OM added and microbial activity. However, the time of maximum aggregation after C addition depends on the soil and substrate investigated. Moreover, the results suggest that the primary macroaggregates, formed within the first 7 d, are still unstable and oversaturated with OM and therefore act as C source for microbial decomposition processes.     

Clay mineralogy determines the importance of biological versus abiotic processes for macroaggregate formation and stabilization

Plant residues, living roots and microbial activity play an important role in aggregate formation and the stabilization of soil organic carbon (SOC), but their impact might differ among soils with different clay mineralogy. We investigated the effect of these organic agents on aggregation and SOC during a 76‐day incubation of 2‐mm sieved soil from an illitic Kastanozem and a kaolinitic Ferralsol, subjected to the following treatments: (i) control (no residue input or plant growth), (ii) residue input, (iii) living plants, and (iv) residue input and living plants. After 46 and 76 days, aggregate size distribution, aggregate‐associated SOC and microbial‐C were measured. In both soils, microbial‐C was less in the control than in the residue and/or plant treatments. After 46 days, new large macroaggregates (> 2000 µm) were formed in the control treatment of the kaolinitic soil, but not of the illitic soil. Control macroaggregates in the kaolinitic soil were formed out of silt and clay particles without accumulating C. Residue input and plant growth had a greater positive effect on macroaggregate formation in the illitic than in the kaolinitic soil. A stronger relation was found between microbial‐C and amount of large macroaggregates in the illitic than in the kaolinitic soil. We conclude that kaolinitic soils can rapidly form macroaggregates independent of biological processes due to physical or electrostatic interactions between the 1:1 clay minerals and oxides. However, biological processes led to stronger organic bonds between the illite compared with the kaolinite clay, resulting in more macroaggregates with long‐term stability in the illitic than in the kaolinitic soil.     

Distribution of microbial biomass and its activity in different soil aggregate size classes as affected by cultivation

Cultivation is known to influence the organic matter status and structural stability of soil. We investigated the effects of 69 yr of cultivation on the nature, distribution and activity of microbial biomass (MB) in different aggregate size classes of an Orthic Brown Chernozemic soil. Cultivation decreased MB content, its activity and enzyme activity in soil. Microaggregate (<0.25mm) size classes in both native and cultivated soils contained lower organic-C, MB-C, fungal biomass, arylsulfatase, acid phosphatase and respiratory activities as compared to macroaggregates. However, the negative effects of cultivation were more pronounced on macroaggregate size classes. Nutrient ratios of both whole aggregates and microbial biomass were narrower in aggregates from cultivated soil as compared to native soil. In both native and cultivated soils, mineralization of C. N and S was greater in macroaggregates as compared to that in microaggregates. The greatest effect of cultivation on nutrient and microbial characteristics was observed in the 0.25 to 1.00 mm dia size classes. These results suggest that microbial biomass, especially fungal biomass, plays an important role in the formation of macroaggregates and is the labile organic matter that serves as the primary source of C and nutrients released following cultivation.     

Biostimulation of indigenous microbial communities for anaerobic transformation of pentachlorophenol in paddy soils of southern China

This study explored biostimulation mechanisms with an electron donor and a shuttle for accelerating pentachlorophenol (PCP) transformation in iron-rich soils. The results indicated that indigenous microbial communities are important for PCP transformation in soils. Biostimulation of indigenous microbial communities by the addition of lactate and anthraquinone-2,6-disulfonate (AQDS) led to the enhanced rates of PCP dechlorination by the dechlorinating- and iron-reducing bacteria in soils. The electrochemical studies using cyclic voltammograms and microbial current measurements confirmed the high reduction potential and the large amount of electrons generated under biostimulation conditions, which were responsible for the higher rates of PCP transformation. After biostimulation treatments by the additions of lactate and/or AQDS during PCP dechlorination processes, microbial community analysis by the terminal restriction fragment length polymorphism (T-RFLP) method showed the abundance terminal restricted fragments (T-RFs), an indicator of bacterial abundance, which represents the dechlorinating- and iron-reducing bacteria, suggesting their critical roles in PCP dechlorination in soils.     

Changes in soil aggregation and microbial community structure control carbon sequestration after afforestation of semiarid shrublands

Changes in plant cover after afforestation induce variations in litter inputs and soil microbial community structure and activity, which may promote the accrual and physical-chemical protection of soil organic carbon (SOC) within soil aggregates. In a long-term experiment (20 years) we have studied the effects, on soil aggregation and SOC stabilization, of two afforestation techniques: a) amended terraces with organic refuse (AT), and b) terraces without organic amendment (T). We used the adjacent shrubland (S) as control. Twenty years after stand establishment, aggregate distribution (including microaggregates within larger aggregates), sensitive and slow organic carbon (OC) fractions, basal respiration in macroaggregates, and microbial community structure were measured. The main changes occurred in the top layer (0–5 cm), where: i) both the sensitive and slow OC fractions were increased in AT compared to S and T, ii) the percentage and OC content of microaggregates within macroaggregates (Mm) were higher in AT than in S and T, iii) basal respiration in macroaggregates was also higher in AT, and iv) significant changes in the fungal (rather than bacterial) community structure were observed in the afforested soils (AT and T) – compared to the shrubland soil. These results suggest that the increase in OC pools linked to the changes in microbial activity and fungal community structure, after afforestation, promoted the formation of macroaggregates – which acted as the nucleus for the formation and stabilization of OC-enriched microaggregates.