Artificial neural network modeling of microbial community structures in the Atlantic Forest of Brazil

Microbial communities vary across the landscape in forest soils, but prediction of their biomass and composition is a difficult challenge due to the large numbers of variables that influence their community structures. Here we examine the use of artificial neural network (ANN) models for extraction of patterns among soil chemical variables and microbial community structures in forest soils from three regions of the Atlantic Forest of Brazil. At each location, variations in soil chemical properties and FAME profiles of microbial community structures were mapped at 20 × 20 m intervals within 10 ha parcels. Geostatistical analyses showed that spatial variability in soil physical and chemical variables could be mapped at scale distances of 20 m, but that FAME profiles representing the microbial communities were highly variable and had no spatial dependence at the same scale in most cases. RDA analysis showed that FAME signatures representing different microbial groups were positively associated with soil pH, OM, P and base cations concentrations, whereas microbial biomass was negatively associated with the same environmental factors. In contrast, ANN models revealed clear relationships between microbial community structures at each parcel location, and generated verifiable predictions of variations in FAME profiles in relation to soil pH, texture, and the relative abundances of base cations. The results suggest that ANN modeling provides a useful approach for describing the relationships between microbial community structures and soil properties in tropical forest soils that were not able to be captured using geostatistical and RDA analyses.     

Biodiversity and trophic structure of soil nematode communities are altered following woody plant invasion of grassland

Woody plant encroachment is an important land cover change in dryland ecosystems throughout the world, and frequently alters above and belowground primary productivity, hydrology, and soil microbial biomass and activity. However, there is little known regarding the impact of this geographically widespread vegetation change on the biodiversity and trophic structure of soil fauna. Nematodes represent a major component of the soil microfauna whose community composition and trophic structure could be strongly influenced by the changes in ecosystem structure and function that accompany woody encroachment. Our purpose was to characterize nematode community composition and trophic structure along a grassland to woodland chronosequence in the Rio Grande Plains of southern Texas. Research was conducted at the La Copita Research Area where woody encroachment has been documented previously. Soil cores (0–10 cm) were collected in fall 2006 and spring 2007 from remnant grasslands and woody plant stands ranging in age from 15 to 86 years, and nematodes were extracted by sugar centrifugation. Neither nematode densities (3200–13,800 individuals kg⁻¹ soil) nor family richness (15–19 families 100 g⁻¹ soil) were altered by woody encroachment. However, family evenness decreased dramatically in woody stands >30 years old. This change in evenness corresponded to modifications in the trophic structure of nematode communities following grassland to woodland conversion. Although root biomass was 2–5× greater in wooded areas, root-parasitic nematodes decreased from 40% of all nematodes in grasslands to <10% in the older wooded areas, suggesting the quality (C:N or biochemical defenses) of woody plant root tissue could be limiting root-parasites. In contrast, bacterivores increased from 30% of nematodes in grasslands to 70–80% in older woody patches. This large increase in bacterivores may be a response to the 1.5–2.5× increase in soil microbial biomass (bacteria + fungi) following woody encroachment. Therefore, while energy flow through grassland nematode communities appears to be distributed nearly equally among herbivory, fungivory and bacterivory, the energy flow through nematode communities in wooded areas appears to be based primarily on bacterivory. We speculate that these shifts in nematode community composition and trophic structure could have important implications for ecosystem patterns and processes. First, the low abundance of root-parasitic nematodes (and presumably root herbivory) under woody plants may be one mechanism by which woody plants are able to establish and compete effectively with grasses during succession from grassland to woodland. Second, the large increase in bacterivores following woody encroachment likely accelerates microbial turnover and the mineralization of N, thereby providing a feedback that enables the persistence of N-rich woody plant communities.     

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.     

城乡复合生态系统土壤微生物群落特征及功能差异

土壤微生物在陆地生态系统多个过程中发挥着重要作用,而城市化过程使得城市及其周边地区土地利用发生剧烈变化,形成了异质性环境梯度,直接或间接地影响了土壤微生物群落的组成和功能,进而影响了其承载的生态系统服务。本文综述了城乡复合生态系统不同景观单元土壤微生物群落的组成特征、主要影响因素及其功能差异,发现城市化对土地利用的改变驱动了土壤微生物群落的组成、结构和功能差异,土地利用、土壤污染物、植被覆盖、土壤性质等因素共同影响土壤微生物群落,并且在不同景观中影响土壤微生物的主导因素有所不同。进一步探讨了土壤微生物的生态服务功能,并分析了不同景观中土壤微生物功能存在的差异性。今后需进一步解析社会—经济—自然复合生态系统格局特征对土壤微生物的影响,揭示城乡复合生态系统不同功能区土壤微生物对土壤生态服务的产生和维持机制,明确变化环境下土壤微生物对土壤安全和人类健康的维持机制,以提升土壤生态服务功能、维护城乡土壤安全和人居环境健康。     

Compaction of forest soils with heavy logging machinery affects soil bacterial community structure

Soil compaction is widespread but tends to be most prevalent where heavy machinery is used in landfill sites, agriculture and forestry. Three forest sites strongly disturbed by heavy logging machinery were chosen to test the physical effects of different levels of compaction on soil bacterial community structure and soil functions. Community analysis comprised microbial biomass C and T-RFLP genetic profiling. Machine passes, irrespective of the compaction level, considerably modified soil structural characteristics at two soil depths (5–10 cm; 15–20 cm). Total porosity decreased up to 17% in the severe compaction. Reflected in this overall decline were large decreases in macroporosity (>50 μm). Reduction in macroporosity was associated with higher water retention and restricted gas exchange in compacted soils. The strongest effect was observed in the severely compacted wheel tracks where air and water conductivities were reduced permanently to 10% or even lower of the original conductivities of undisturbed soils. Very slow drainage in combination with a dramatically reduced gas permeability led to unfavorable soil conditions in severely disturbed traffic lanes reflecting the changes in the total bacterial community structures at both soil depths. Additionally, microbial biomass C tended to be lower in compacted soil. Our results indicate that the type of severe treatments imposed at these forest sites may have strong adverse effects on long-term soil sustainability.     

Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies

Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine links between the variability of parameters, utilising two sampling strategies. The first (design 1) involved extracting 25 cores from random locations throughout the field and pooling them into five sets of five cores. The second (design 2) involved a further 25 cores within five 1 m² sub-plots. Sub-samples from each sub-plot were pooled in order to determine between and within sub-plot variability. All samples were analysed independently and as pooled sub-samples. Results indicate that pooling spatially separated samples significantly reduced the variability in pH, compared to individual samples. Pooling samples from a small area resulted in lower within sub-plot variability than between sub-plots for pH and bacterial community composition assessed by terminal-restriction fragment length polymorphism analysis. Following multivariate statistical analysis, a large amount of variation in community composition was explained by soil pH, which is remarkable given the relatively small size of the sampling area and minor differences in pH. Moisture content was also important in determining bacterial communities in the random design (design 1). In the 1 m² sub-plot design (design 2), the spatial location of the plots explained a large degree of the variation in bacterial community composition between plots, which was due to spatial autocorrelation of pH and possible additional environmental parameters. This study emphasises the importance of sampling design for obtaining representative samples from soil.     

Changes of the functional diversity of soil microbial community during the colonization of abandoned grassland by a forest

The impact of secondary succession of grassland communities towards a Norway spruce forest on soil microbial community was studied on a belt transect established in the Pol’ana Mts., Central Europe. Data on understory vegetation, light availability, soil properties and microbial activity were collected on 147 plots distributed over regular grid. Moreover, distributions of functional groups of microorganisms were assessed using BIOLOG analysis on a subset of 27 plots. Mantel partial correlations between microbial community indicators and environmental variables showed that microbial activity generally decreased with increasing tree density and size, whereas it increased with increasing radiation at the soil surface, soil temperature, and cover and diversity of understory vegetation. Functional richness and diversity of microorganisms were positively correlated with solar radiation, but also with plant species richness and diversity. Abundance of several functional groups correlated closely with succession-related variables. Redundance analysis of microbial data provided slightly different outcomes. Forward selection yielded only two environmental variables significantly influencing the composition of the microbial community: tree influence potential and organic carbon content. Abundances of several functional microbial groups correlated with tree influence, documenting that microbial community changes are at least partially driven by the colonization of grassland by trees. Nevertheless, the relative importance of abiotic environment change and plant community succession on microbial community dynamics remains unresolved.     

Spatial analysis reveals differences in soil microbial community interactions between adjacent coniferous forest and clearcut ecosystems

Knowledge of how forest management influences soil microbial community interactions is necessary for complete understanding of forest ecology. In this study, soil microbial communities, vegetation characteristics and soil physical and chemical properties were examined across a rectangular 4.57 × 36.58 m sample grid spanning adjacent coniferous forest and clearcut areas. Based on analysis of soil extracted phospholipid fatty acids, total microbial biomass, fungi and Gram-negative bacteria were found to be significantly reduced in soil of the clearcut area relative to the forest. Concurrent with changes in microbial communities, soil macroaggregate stability was reduced in the clearcut area, while no significant differences in soil pH and organic matter content were found. Variography indicated that the range at which spatial autocorrelation between samples was evident (patch size) was greater for all microbial groups analyzed in the clearcut area. Overall, less spatial structure could be resolved in the forest. Variance decomposition using principal coordinates of neighbor matrices spatial variables indicated that soil aggregate stability and vegetation characteristics accounted for significant microbial community spatial variation in analyses that included the entire plot. When clearcut and forest areas were analyzed separately, different environmental variables (pH in the forest area and soil organic matter in the clearcut) were found to account for variation in soil microbial communities, but little of this variation could be ascribed to spatial interactions. Most microbial variation explained by different components of microbial communities occurred at spatial scales other than those analyzed. Fungi accounted for over 50% of the variation in bacteria of the forest area but less than 11% in the clearcut. Conversely, AMF accounted for significant variation in clearcut area, but not forest, bacteria. These results indicate broadly disparate controls on soil microbial community composition in the two systems. We present multiple lines of evidence pointing toward shifts in fungi functional groups as a salient mechanism responsible for qualitative, quantitative and spatial distribution differences in soil microbial communities.     

Dynamics of soil microbial biomass C, N and P in disturbed and undisturbed stands of a tropical wet-evergreen forest

To understand the spatial and temporal dynamics of soil microbial biomass and its role in soil organic matter and nutrient flux in disturbed tropical wet-evergreen forests, we determined soil microbial biomass C, N and P at two soil depths (0–15 and 15–30 cm), along a disturbance gradient in Arunachal Pradesh, northeastern India. Disturbance resulted in considerable increase in air temperature and light intensity in the forest and decline in the soil nutrients concentration, which affected the growth of microbial populations and soil microbial biomass. There were significant correlations between bacterial and fungal populations and microbial biomass C, N and P. Soil microbial population was higher in the undisturbed (UD) forest stand than the disturbed forest stands during post-monsoon and less during rainy season due to heavy rainfall. Greater demand for nutrients by plants during rainy season limited the availability of nutrients to soil microbes and therefore, low microbial biomass C, N and P. Microbial biomass was negatively correlated with soil temperature and pH in all the forest stands. However, there were significant positive relationships among microbial biomass C, N and P. Percentage contribution of microbial C to soil organic C was higher in UD forest, whereas percentage contribution of microbial biomass N and P to total N and total P was higher in the moderately disturbed site than in the highly disturbed (HD) site. These results reveal that the nutrient retention by soil microbial biomass was greater in the selective logged stand and would help in the regeneration of the forest upon protection. On the other hand, the cultivated site (HD) that had the lowest labile fractions of soil organic matter may recover at a slower phase. Further, minimum and maximum microbial biomass C, N and P during rainy and winter seasons suggest the synchronization between nutrient demand for plant growth and nutrient retention in microbial biomass that would help in ecosystem recovery following disturbance.     

Exploring soil microbial communities and soil organic matter: Variability and interactions in arable soils under minimum tillage practice

This study describes an integrated approach (1) to monitor the quantity and quality of water extractable organic matter (WEOM) and size, structure and function of microbial communities in space (depth) and time, and (2) to explore the relationships among the measured properties. The study site was an arable field in Southern Germany under integrated farming management including reduced tillage. Samples of this Eutric Cambisol soil were taken in July 2001, October 2001, April 2002 and July 2002 and separated into three depths according to the soil profile (0–10 cm, 10–28 cm and 28–40 cm). For each sample, the quantity and quality (humification index, HIX) of water extractable organic matter (WEOM) were measured concomitantly with soil enzyme activities (alkaline phosphatase, β-glucosidase, protease) and microbial community size (C_mic). Furthermore, microbial community structure was characterised based on the fingerprints of nucleic acids (DNA) as well as phospholipid fatty acids (PLFA). We observed strong influences of sampling date and depth on the measured parameters, with depth accounting for more of the observed variability than date. Increasing depth resulted in decreases in all parameters, while seasonal effects differed among variants. Principal component (PC) analysis revealed that both DNA and PLFA fingerprints differentiated among microbial communities from different depths, and to a smaller extent, sampling dates. The majority of the 10 PLFAs contributing most to PC 1 were specific for anaerobes. Enzyme activities were strongly related to C_mic, which was depending on water extractable organic carbon and nitrogen (WEOC and WEON) but not to HIX. HIX and WEOM interact with the microbial community, illustrated by (1) the correlation with the number of PLFA peaks (community richness), and (2) the correlations with community PC analysis scores.     

Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China

Background, Aims, and Scope  Knowledge about shifts of microbial community structure and diversity following different agricultural management practices could improve our understanding of soil processes and thus help us to develop sound management strategies. A long-term fertilization experiment was established in 1989 at Fengqiu (35°00′N, 114°24′E) in northern China. The soil (sandy loam) is classified as aquic inceptisols and has received continuous fertilization treatments since then. The fertilization treatments included control (CK, no fertilizer), chemical fertilizers nitrogen (N) and potassium (K) (NK), phosphorous (P) and K (PK), NP, NPK, organic manure (OM), and half chemical fertilizers NPK plus half organic manure (1/2NPKOM). The objective of this study was to examine if the microbial community structure and diversity were affected by the long-term fertilization regimes. Materials and Methods  Soil samples were collected from the long-term experimental plots with seven treatments and four replications in April 2006. Microbial DNAs were extracted from the soil samples and the 16S rRNA genes were PCR amplified. The PCR products were analyzed by DGGE, cloning and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and the clone libraries constructed from the excised DGGE bands. Results  The bacterial community structure of the OM and PK treatments were significantly different from those of all other treatments. The bacterial community structures of the four Ncontaining treatments (NK, NP, NPK and 1/2NPKOM), as well as CK, were more similar to each other. The changes in bacterial community structures of the OM and PK treatments showed higher richness and diversity. Phylogenetic analyses indicated that Proteobacteria (30.5%) was the dominant taxonomic group of the soil, followed by Acidobacteria (15.3%), Gemmatimonadetes (12.7%), etc. Discussion  Irrespective of the two fertilization treatments of OM and PK, the cluster analysis showed that bacterial communities of the remaining five treatments of CK, NK, NP, NPK and 1/2NPKOM seemed to be more similar to each other, which indicated the relatively weak effects of the four N-containing treatments on soil bacterial communities. N fertilizer may be considered as a key factor to counteract the effects of other fertilizers on microbial communities. Conclusions  Our results show that long-term fertilization regimes can affect bacterial community structure and diversity of the agricultural soil. The OM and PK treatments showed a trend towards distinct community structures, higher richness and diversity when compared to the other treatments. Contrasting to the positive effects of OM and PK treatments on the bacterial communities, N fertilizer could be considered as a key factor in the soil to counteract the effects of other fertilizers on soil microbial communities. Recommendations and Perspectives  Because of the extremely high abundance and diversity of microorganisms in soil and the high heterogeneity of the soil, it is necessary to further examine the effects of fertilization regimes on microbial community and diversity in different type soils for comprehensively understanding their effects through the appropriate combination of molecular approaches. ESS-Submission Editor: Chengrong Chen, PhD (c.chen@griffith.edu.au)     

Influence of irrigated agriculture on soil microbial diversity

Organic carbon (C), bacterial biomass and structural community diversity were measured in Southern Idaho soils with long term cropping histories. The soils tested were native sagebrush vegetation (NSB), irrigated moldboard plowed crops (IMP), irrigated conservation – chisel – tilled crops (ICT) and irrigated pasture systems (IP). Organic C concentration in soils decreased in the order NSB 0–5 cm > IP 0–30 cm = ICT 0–15 cm > IMP 0–30 cm > NSB 5–15 cm = NSB 15–30 cm. Active bacterial, fungal and microbial biomass correlated with soil C as measured by the Walkely Black method in positive curvilinear relationships (r² = 0.93, 0.80 and 0.76, respectively). Amplicon length heterogeneity (LH-PCR) DNA profiling was used to access the eubacterial diversity in all soils and at all depths. The Shannon–Weaver diversity index was used to measure the differences using the combined data from three hypervariable domains of the eubacterial 16S rRNA genes. Diversity was greatest in NSB 15–30 cm soil and lowest in the IMP soil. With the exception of IMP with the lowest diversity index, the samples highest in C (NSB 0–5 cm, IP 0–30 cm, ICT 0–15 cm) reflected lower diversity indices. However, these indices were not significantly different from each other. ICT and IP increase soil C and to some extent increase diversity relative to IMP. Since soil bacteria respond quickly to environmental changes, monitoring microbial communities may be one way to assess the impact of agricultural practices such as irrigation and tillage regimes.     

Nematode community composition and diversity associated with a topoclimatic transect in a rain shadow desert

The effect of a topoclimatic gradient on soil nematode communities was investigated in the Israeli Judean Desert. Four locations along a 35 km gradient, from an elevation of 650 m above sea level with 620 mm rainfall to a –60 m relative to sea level with a rainfall below 110 m, were studied: Givat Yearim, Maale Adumim, Mishor Adumim and Kalia. Monthly soil samples were collected between January 1994 and December 1995. Thirteen nematode families and 17 genera were observed. Cephalobus, Heterocephalobus, Aphelenchoides, Tylenchus, Dorylaimus and Eudorylaimus were found to be the dominant genera. Ecological measurements of soil nematode community structure, diversity, and maturity indices were assessed, and comparisons between four locations and four seasons were made. Significant differences in the total numbers of nematodes were found between the locations (p < 0.01) and seasons (p < 0.05), where Givat Yearim > Maale Adumim > Mishor Adumim > Kalia, winter > spring > autumn > summer. Bacterivores were found to be the most abundant trophic group across locations and seasons, with a mean relative abundance of 55.0%. The densities of bacterivores, plant parasites and omnivores-predators during the winter season exhibited similar trends at all four locations, with Givat Yearim > Maale Adumim > Mishor Adumim > Kalia. None of the ecological indices were significantly different between locations. However, the maturity index (MI), trophic diversity (TD) and Simpson diversity (SI) exhibited significant differences between seasons.     

Effect of di-(2-ethylhexyl) phthalate (DEHP) on microbial biomass C and enzymatic activities in soil

The effects of di-(2-ethylhexyl) phthalate (DEHP) at five different doses from 10 to 1000 mg kg⁻¹ soil on biological properties were investigated over a period of 56 days. Meanwhile, the dissipation of DEHP was also monitored. The results indicated that the microbial biomass C (C_mic) fluctuated at around 70 mg kg⁻¹ soil for the control, whereas the C_mic varied significantly for the soil samples contaminated by DEHP. The catalase activities in all five treatments were stimulated at most time, and the activities of phosphatase in the soils treated by DEHP with 500 mg kg⁻¹ or 1000 mg kg⁻¹ were significantly higher than the other treatments from the 20th day. Urease was more sensitive and inhibited significantly during the initial period of incubation. Additionally, the dose–response relationship of invertase was presented in the later phase of incubation. The activities of urease and invertase might indicate soil perturbations caused by the introduction of DEHP. The dissipation of DEHP was found to follow the pseudo first-order kinetics behavior.     

中国北方温带草原土壤微生物对气温变暖与添加氮素的响应特征

The responses of soil microbes to global warming and nitrogen enrichment can profoundly affect terrestrial ecosystem functions and the ecosystem feedbacks to climate change. However, the interactive effect of warming and nitrogen enrichment on soil microbial community is unclear. In this study, individual and interactive effects of experimental warming and nitrogen addition on the soil microbial community were investigated in a long-term field experiment in a temperate steppe of northern China. The field experiment started in 2006 and soils were sampled in 2010 and analyzed for phospholipid fatty acids to characterize the soil microbial communities. Some soil chemical properties were also determined. Five-year experimental warming significantly increased soil total microbial biomass and the proportion of Gram-negative bacteria in the soils. Long-term nitrogen addition decreased soil microbial biomass at the 0-10 cm soil depth and the relative abundance of arbuscular mycorrhizal fungi in the soils. Little interactive effect on soil microbes was detected when experimental warming and nitrogen addition were combined. Soil microbial biomass positively correlated with soil total C and N, but basically did not relate to the soil C/N ratio and pH. Our results suggest that future global warming or nitrogen enrichment may significantly change the soil microbial communities in the temperate steppes in northern China.     

Short-range spatial variability of soil physico-chemical variables related to earthworm clustering in a neotropical gallery forest

In this study, we investigated the spatial distribution of an earthworm community together with the heterogeneity of selected soil properties in a gallery forest (GF) of the Colombian “Llanos”. We performed fine-scale spatial variability by intensively sampling 100 points distributed in the nodes of a regular grid with 5 m inter-sample distance. Non-parametric statistics were used and included SADIE analysis and partial Mantel test, in addition to geostatistics (semi-variograms) and correlogram computation. Our results indicated that the spatial distribution of earthworms was characterized by areas of presence (patches) and absence (gaps), although the general pattern was random at the scale of this study (<5 m), while soil physico-chemical characteristics showed a clumped spatial distribution. Contrary to previous results reported for the nearby savanna, a significant spatial association was found for two competing endogeic species Andiodrilus sp. and Glossodrilus sp. in the GF. Semi-variograms of soil environmental factors were adjusted to model families most commonly used (spherical and linear), and correlograms for earthworms showed significant positive and negative spatial autocorrelation for lag distances <15 m and >30 m, respectively. Partial Mantel test revealed specific significant relationships between soil variables and some species. The earthworm community of the GF displayed a random structure in a spatially clumped soil environment, and our results suggested that spatial distribution observed for some species could be the result of preferential selection of soil environmental factors. In other words, soil heterogeneity contributed to the formation of population patches for some earthworm species. The variability of suitable sites (resource availability patchiness) exerted an influence in the spatial distribution of earthworms at the scale used in this study, and we identified the spatial scale at which both environmental heterogeneity could influence and express earthworm impact on soil properties.     

滩涂土壤固氮菌群落与环境因子的典范对应分析

选择连续4年进行水稻–紫云英轮作的田块,在0~10、10~20、20~40和40~80 cm剖面深度分别采集土样,利用PCR-DGGE技术分析水稻–紫云英轮作对土壤不同剖面深度固氮菌nif H基因丰度与群落多样性的影响,并对固氮菌群落与8个环境因子进行了典范对应分析(CCA)。试验结果表明,水稻–紫云英轮作能提高滩涂土壤固氮菌的丰度和多样性。水稻-紫云英轮作处理10~20 cm土壤剖面中固氮菌丰度最大,水稻–休闲处理40~80 cm土壤剖面中的最小,其Shannon-Weaver多样性指数分别为3.18和1.51。滩涂土壤环境因子中,总氮与NH_4~+-N、EC与有效磷、pH与速效钾,两两之间的相关性最高;CCA排序图表明土壤有机质、NH_4~+-N和有效磷是影响滩涂土壤固氮菌群落的主要因子。     

Changes in soil microbial community structure following the abandonment of agricultural terraces in mountainous areas of Eastern Spain

In Eastern Spain, almond trees have been cultivated in terraced orchards for centuries, forming an integral part of the Mediterranean forest scene. In the last decades, orchards have been abandoned due to changes in society. This study investigates effects of changes in land use from forest to agricultural land and the posterior land abandonment on soil microbial community, and the influence of soil physico-chemical properties on the microbial community composition (assessed as abundances of phospholipids fatty acids, PLFA). For this purpose, three land uses (forest, agricultural and abandoned agricultural) at four locations in SE Spain were selected. Multivariate analysis showed a substantial level of differentiation in microbial community structure according to land use. The microbial communities of forest soils were highly associated with soil organic matter content. However, we have not found any physical or chemical soil property capable of explaining the differences between agricultural and abandoned agricultural soils. Thus, it was suggested that the cessation of the perturbation caused by agriculture and shifts in vegetation may have led to changes in the microbial community structure. PLFAs indicative of fungi and ratio of fungal to bacterial PLFAs were higher in abandoned agricultural soils, whereas the relative abundance of bacteria was higher in agricultural soils. Actinomycetes were generally lower in abandoned agricultural soils, while the proportions of vesicular–arbuscular mycorrhyzal fungi were, as a general trend, higher in agricultural and abandoned agricultural soils than in forests. Total microbial biomass and richness increased as agricultural < abandoned agricultural < forest soils.     

Comparative mycobiotic and edaphic analyses of two neighboring soil profiles on different lithologies in Upper Galilee, Israel

Microfungal communities from two profiles of the neighboring pale rendzina and basaltic vertisoil in the Upper Galilee area, Israel, were analyzed and compared. The bedrock lithology determines the key differences in mineralogical composition of the contrasting soils on chalk and basaltic rocks. Pale rendzina on chalk is strongly calcareous while the basaltic soil profile is leached from carbonates below the 5–8 cm depth and is significantly magnetically enhanced. The soils also differ in CEC, exchangeable cations, and in microstructure. In parallel, mycobiota isolated by the soil dilution plate method (124 species) displays different patterns both in distribution along the contrasting profiles and in structure of the communities at definite depths. The basaltic mycobiota is significantly richer (87 vs. 69 species in the rendzina) being less heterogeneous and even at a 5–50 cm depth. According to all estimated mycobiotic characteristics, at 15–18 cm depth the differences between the basaltic and rendzina soils are mostly pronounced. Excellent aeration of the basaltic soil in contrast to the rendzina may account at least partly for the peak of mycobiotic differences at this depth. No single edaphic parameter is responsible for the greatest level of variations in the mycobiotic characteristics indicating that co-influence of soil biotic/abiotic factors determined distribution of microfungi throughout the profiles.     

Changes in the soil microbial community structure with latitude in eastern China, based on phospholipid fatty acid analysis

Phospholipid fatty acid (PLFA) profiles were measured in soils from 14 sites in eastern China representing typical geographic zones of varying latitude from north (47.4°N) to south (21.4°N). Amounts of soil microbial biomass, measured as total amounts of PLFAs, showed no regular trend with latitude, but were positively correlated with soil organic carbon content, the concentration of humic acid and amorphous iron oxide. Soil microbial community structure showed some biogeographical distribution trends and was separated into three groups in a cluster analysis and principal coordinate analysis of log transformed PLFA concentrations (mol%). Soils in the first group came from northern China with medium mean annual temperature (1.2–15.7 °C) and rainfall (550–1021 mm). Soils in the second group originated from southern China with a relatively higher mean annual temperature (15.7–21.2 °C) and rainfall (1021–1690 mm). Soils clustered in the third group originated from the most southerly region. The northern soils contained relatively more bacteria and Gram-negative PLFAs, while the southern soils had more fungi and pressure indexed PLFAs. These differences in soil microbial community structure were largely explained by soil pH, while other site and soil characteristics were less important.