Bacterial community structure and activity in different Cd-treated forest soils

In this study we compared indicators of Cd bioavailability (water extracts, Lakanen extracts, free ions) and ecotoxicity in forest soils with contrasting physico-chemical characteristics. Soil samples were treated with CdCl(2) solutions (0, 0.1, 1, 10 and 100 mM) and incubated for 30 days. Microbial activity indexes (acid phosphatase, beta-glucosidase, basal respiration) and changes in bacterial community structure using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting were investigated. The Cd concentrations measured ranged from 1% to 37% of the total additions in water extracts, to higher levels in Lakanen extracts. Effects of Cd were observed at bioavailable concentrations exceeding United Nations/European Economic Commission UN/ECE guidelines for total Cd in the soil solution. Basal respiration was the most affected index, while enzymatic activities showed variable responses to the Cd treatments. We also noticed that soils with pH higher than 6.7 and clay content higher than 50% showed inhibition of basal respiration but no marked shift in bacterial community structure. Soils with lower pH (pH <5.8) with less clay content (<50%) showed in addition strong changes in the bacterial community structure. Our results provide evidence for the importance of relating the effects of Cd on the soil communities to soil properties and to bioavailability.     

Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils

Background

Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition.

Methodology/Principal Findings

We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found.

Conclusions/Significance

Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH.     

河南宝天曼不同林龄与林型森林土壤的细菌群落结构与多样性

采用高通量16S rRNA标签测序法,比较了地处北亚热带与暖温带过渡带的宝天曼自然保护区不同林龄与林分类型的土壤细菌群落结构及多样性.结果表明： 宝天曼森林土壤细菌以变形菌门(29%)、酸杆菌门(18.5%)、疣微菌门(10%)等为主,共检测到60门1209属,优势属主要有疣微菌门的DA101(6.3%)、酸杆菌门的Acidobacteria 2(5.9%)和Candidatus Solibacter(2.9%)、泉古菌门的Candidatus Nitrososphaera(2.6%)等.不同林龄和林分类型土壤分别具有特有的种属组成及高丰度和低丰度种属.林龄与林分类型都对土壤微生物群落结构影响显著,且林分类型的影响大于林龄.80年林龄的锐齿栎土壤菌群多样性在不同林龄和林分类型中均最低.pH、土壤全氮、有机碳等是不同林龄及林分类型下土壤菌群结构变化的重要影响因子.     

Bacterial colonization of minerals in grassland soils is selective and highly dynamic

Bacteria colonize reactive minerals in soils where they contribute to mineral weathering and transformation. So far, the specificity, patterns and dynamics of mineral colonization have rarely been assessed under natural conditions. High throughput Illumina sequencing was employed to investigate the bacterial communities assembling on illite and goethite during exposure to natural grassland soils. Two different types of organic carbon sources, simple carbon compounds representing root exudates and detritus of two dominant grassland plant species were applied, and their effects on the temporal dynamics of bacterial communities were investigated. The observed temporal patterns suggest that the surfaces of de novo exposed minerals in soils drive the establishment of bacterial communities and override the effect of the type of carbon sources and of other environmental properties. Mineral colonization was selective and specific bacterial sequence variants exhibited distinct colonization patterns, among which early, intermittent, and late colonizers could be distinguished. Based on our results, soil minerals are not only colonized by specific bacterial communities but enable a succession of different bacterial communities. Our results thereby expand the concept of the mineralosphere and provide novel insights into mechanisms of community assembly in the soil ecosystem.     

Drivers of microbial community structure in forest soils

Applied Microbiology and Biotechnology - Forests are essential biomes for global biogeochemical cycles, and belowground microorganisms have a key role in providing relevant ecosystem services. To...     

Dissolved organic carbon chemistry and dynamics in contrasting forest and grassland soils

Seasonal variability in biogeochemical signatures was used to elucidate the dominant pathways of soil microbial metabolism and elemental cycling in an oligotrophic mangrove system. Three interior dwarf mangrove habitats (Twin Cays, Belize) where surface soils were overlain by microbial mats were sampled during wet and dry periods of the year. Porewater equilibration meters and standard biogeochemical methods provided steady-state porewater profiles of pH, chloride, sulfate, sulfide, ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, nitrogen, and phosphorus, reduced iron and manganese, dissolved inorganic carbon, methane and nitrous oxide. During the wet season, the salinity of overlying pond water and shallow porewaters decreased. Increased rainwater infiltration through soils combined with higher tidal heights appeared to result in increased organic carbon inventories and more reducing soil porewaters. During the dry season, evaporation increased both surface water and porewater salinities, while lower tidal heights resulted in less reduced soil porewaters. Rainfall strongly influenced inventories of dissolved organic carbon and nitrogen, possibly due to more rapid decay of mangrove litter during the wet season. During both times of year, high concentrations of reduced metabolites accumulated at depth, indicating substantial rates of organic matter mineralization coupled primarily to sulfate reduction. Nitrous oxide and methane concentrations were supersaturated indicating considerable rates of nitrification and/or incomplete denitrification and methanogenesis, respectively. More reducing soil conditions during the wet season promoted the production of reduced manganese. Contemporaneous activity of sulfate reduction and methanogenesis was likely fueled by the presence of noncompetitive substrates. The findings indicate that these interior dwarf areas are unique sites of nutrient and energy regeneration and may be critical to the overall persistence and productivity of mangrove-dominated islands in oligotrophic settings.     

Carbon isotopic fractionation in subtropical brazilian grassland soils. Comparison with tropical forest soils

The natural relationship¹³C/¹²C determined in three soil profiles under grass vegetation indicated a depletion in organic¹³C at depth: theδ ¹³C was between −18‰ and −15‰ in the A horizons and ranged from −18 to −22‰ at depth. Previous work showed that in forest soils, whereδ ¹³C was near −28‰ in the upper horizon, there was, on the contrary, a relative enrichment of the lower strata. This meant thatδ ¹³C, initially different in the various topsoils, became more equal at depth. Comparison between dark, deep horizons (sombric horizons), which are certainly of illuvial origine, would confirm this:δ ¹³C of grassland and a forest sombric horizon were almost equal at around −22‰. These results might mean that, in natural ecosystems, the isotopic carbon composition of the soil underlying humus would be independent of the vegetation type. This would have practical implications for the use of¹³C as a tracer for soil organic matter studies.     

鼎湖山不同演替阶段森林土壤细菌多样性

[目的]了解鼎湖山早、中、后3个演替阶段的3类森林(针叶林、混交林、阔叶林)土壤细菌群落结构及其多样性,为下一步研究不同演替阶段森林土壤微生物的功能及其与植物的相互作用提供依据.[方法]在代表性林区采集土样,从中提取总DNA,利用细菌通用引物27F和1492R PCR扩增16S rDNA并构建文库.从所构建的3个文库中各挑取150个阳性克隆子并对插入片段进行测序,利用Mothur软件对所得序列进行分析.[结果]从针叶林、混交林和阔叶林文库中分别得到122、118和120条有效16S rDNA序列,各代表70、64、72个OTUs(operational taxonomic units,以97％相似性为划分标准).分析结果显示,共检测到8个细菌门类,其中酸杆菌门(Acidobacteria)在针叶林、混交林和阔叶林土样中分别占53.3％,67.8％和60％ ;变形杆菌门(Proteobacteria)分别占29.5％,20.3％和32.5％ ;其它如厚壁菌,放线菌等均不超过10％.3类森林土壤细菌群落结构差异显著(P＜0.05),3者两两间共有的OTU数量占检测到的OTU总数的比例均低于25％,其中阔叶林土壤细菌有着最高的Chao指数(414.2)和Shannon指数(3.90),及最低的Simpson优势度指数(0.0249).[结论]鼎湖山针叶林、混交林和阔叶林3类林区土壤细菌在种群构成上差异显著,其中阔叶林土壤细菌丰富度及多样性相对较高,但3者在大类组成方面比较相似,均为酸杆菌占绝对优势,变形杆菌次之.     

Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils

Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal–Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts.     

Factors affecting the growth of Eucalyptus delegatensis seedlings in inhibitory forest and grassland soils

In many highland forests of Eucalyptus delegatensis in Tasmania the establishment and healthy growth of eucalypts is promoted and maintained by fire. In the absence of fire, secondary succession from eucalypt forest to rainforest occurs, during which the eucalypts decline and die prematurely. On sites that are prone to radiation frost severe reduction or removal of a tree canopy allows a sward of tussock grasses to develop, in competition with which seedlings of eucalypts decline in growth and a high proportion dies.Factors of the soil that could contribute to these phenomena were investigated by means of pot experiments that used soils from:o     

Nitrogen deposition but not ozone affects productivity and community composition of subalpine grassland after 3 yr of treatment

A field experiment was established at 2000 m above sea level (asl) in the central Swiss Alps with the aim of investigating the effects of elevated ozone (O(3)) and nitrogen deposition (N), and of their combination, on above-ground productivity and species composition of subalpine grassland. One hundred and eighty monoliths were extracted from a species-rich Geo-Montani-Nardetum pasture and exposed in a free-air O(3)-fumigation system to one of three concentrations of O(3) (ambient, 1.2 x ambient, 1.6 x ambient) and five concentrations of additional N. Above-ground biomass, proportion of functional groups and normalized difference vegetation index (NDVI) were measured annually. After 3 yr of treatment, the vegetation responded to the N input with an increase in above-ground productivity and altered species composition, but without changes resulting from elevated O(3). N input > 10 kg N ha(-1) yr(-1) was sufficient to affect the composition of functional groups, with sedges benefiting over-proportionally. No interaction of O(3) x N was observed, except for NDVI; positive effects of N addition on canopy greenness were counteracted by accelerated leaf senescence in the highest O(3) treatment. The results suggest that effects of elevated O(3) on the productivity and floristic composition of subalpine grassland may develop slowly, regardless of the sensitive response to increasing N.     

A comparison of soil quality in adjacent cultivated,forest and native grassland soils

Changes in soil quality after 45 years of continuous production of corn (Zea mays L.) by the conventional tillage method (C) compared with adjacent poplar forest (F) and native grassland (G) sites were examined. The investigated parameters were: total and humified organic C, total N, light fraction content and composition, water-soluble organic C (WSOC), water-soluble carbohydrates (WSC), phenolic substances, biomass C, cumulative CO₂-C (soil respiration) (C _m), enzyme activities (alkaline phosphatase, protease, -glucosidase, urease, catalase and dehydrogenase). Empirical indexes of soil quality were also calculated: biomass C/organic C, specific respiration of biomass C (qCO₂), death rate quotient (qD), metabolic potential (MP), biological index of fertility (BIF), enzyme activity number (EAN) and hydrolysing coefficient (HC). Results indicate that long-term corn production at an intensive level caused a marked decline in all examined parameters. Between the undisturbed systems, native grassland showed higher values of soil quality parameters than forest site. The indexes most responsive to management practices that may provide indications of the effects of soil cultivation, as well as of the differently undisturbed ecosystems were: organic C, WSC, C _m, protease, -glucosidase, urease and HC. Soil enzyme activities were well related with, and not more sensitive than organic carbon.     

Role of topography and soils in grassland structuring at the landscape and community scales

The relative importance of abiotic factors in community assembly is debated and thought to be dependent on the scale. I investigated the relative role of topography and soils as structuring agents at the landscape and the community scales in 126 subalpine calcareous grasslands in the Pyrenees, in terms of species composition and abundance. I wished to know: (1) the role of abiotic factors in the organization of plant communities across the landscape; (2) how much of the variation in community distribution was accounted for by abiotic factors; and (3) how well their role applied to the distribution of dominant species at the landscape and the community scales. The hypothesis was: abiotic factors play an important role in community distribution in the landscape, but species interactions are more important within communities. Multivariate methods generated four communities, organized in two contrasting groups along the main vegetation axis, which explained 13% of the variation: mesic grasslands (Nardus stricta and Festuca nigrescens communities) and xeric grasslands (Carex humilis and Festuca gautieri communities). Mesic communities were more acidic and fertile than xeric communities. Changes in the abiotic environment, accounting for up to 80% of the variation in the vegetation, were smooth, while the transition between xeric and mesic grasslands was sharp in terms of species composition. The distribution in the landscape of the first main species from each community was closely related to abiotic factors, which modeled poorly the abundance of the main species at smaller scales. At the within-community scale, the explanatory power of biotic relationships was community dependent, producing the most significant models for plants highly dominant within their communities, such as N. stricta and F. gautieri. Contrary to current hypothesis, there was a shift from mainly positive relationships among dominant species in fertile mesic communities to mainly negative in infertile xeric ones.     

Bacterial community characterization in the soils of native and restored rainforest fragments

The Brazilian Atlantic Forest (“Mata Atlântica”) has been largely studied due to its valuable and unique biodiversity. Unfortunately, this priceless ecosystem has been widely deforested and only 10 % of its original area is still untouched. Some projects have been successfully implemented to restore its fauna and flora but there is a lack of information on how the soil bacterial communities respond to this process. Thus, our aim was to evaluate the influence of soil attributes and seasonality on soil bacterial communities of rainforest fragments under restoration processes. Soil samples from a native site and two ongoing restoration fragments with different times of implementation (10 and 20 years) were collected and assayed by using culture-independent approaches. Our findings demonstrate that seasonality barely altered the bacterial distribution whereas soil chemical attributes and plant species were related to bacterial community structure during the restoration process. Moreover, the strict relationship observed for two bacterial groups, Solibacteriaceae and Verrucomicrobia, increasing from the more recently planted (10 years) to the native site, with the 20 year old restoration site in the middle, which may suggest their use as bioindicators of soil quality and recovery of forest fragments being restored.     

Bacterial and fungal community structure in Arctic tundra tussock and shrub soils

Fungal and bacterial community structure in tussock, intertussock and shrub organic and mineral soils at Toolik Lake, Alaska were evaluated. Community structure was examined by constructing clone libraries of partial 16S and 18S rRNA genes. The soil communities were sampled at the end of the growing season in August 2004 and just after the soils thawed in June 2005. The communities differed greatly between vegetation types, although tussock and intertussock soil communities were very similar at the phyla level. The communities were relatively stable between sample dates at the phyla and subphyla levels, but differed significantly at finer phylogenetic scales. Tussock and intertussock bacterial communities were dominated by Acidobacteria, while shrub soils were dominated by Proteobacteria. These results appear consistent with previous work demonstrating that shrub soils contain an active, bioavailable C fraction, while tussock soils are dominated by more recalcitrant substrates. Tussock fungi communities had higher proportions of Ascomycota than shrub soils, while Zygomycota were more abundant in shrub soils. Recent documentation of increasing shrub abundance in the Arctic suggests that soil microbial communities and their functioning are likely to be altered by climate change.     

Seasonal influences on fungal community structure in unimproved and improved upland grassland soils

Seasonal and management influences on the fungal community structure of two upland grassland soils were investigated. An upland site containing both unimproved floristically diverse (U4a) and improved mesotrophic (MG7b) grassland types was selected. Samples from both grassland types were taken at five times in one year. Soil fungal community structure was assessed using fungal automated ribosomal intergenic spacer analysis (ARISA), a DNA-profiling approach. A grassland management regime was found to strongly affect fungal community structure, with fungal ARISA profiles from unimproved and improved grassland soils differing significantly. The number of fungal ribotypes found was higher in unimproved than improved grassland soils, providing evidence that improvement may reduce the suitability of upland soil as a habitat for specific groups of fungi. Seasonal influences on fungal community structure were also noted, with samples taken in autumn (October) more correlated with change in ribotype profiles than samples from other seasons. However, seasonal variation did not obscure the measurement of differences in the fungal community structure that were due to agricultural improvement, with canonical correspondence analysis indicating grassland type had a stronger influence on fungal profiles than did season.     

Root controls on soil microbial community structure in forest soils

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0–10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.     

Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils

The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.     

水分对林地和草地土壤氮初级转化速率的影响

水分含量是与土壤氮转化相关微生物活性的重要影响因素。本研究以黑龙江省北安市的草地和林地土壤为对象,通过室内培养试验,利用¹⁵N同位素标记技术和FLUAZ数值优化模型研究60%和100%田间持水量(WHC)条件下土壤氮初级矿化速率、初级固定速率、初级硝化速率和初级反硝化速率,以探讨土壤氮初级转化速率对水分含量变化的响应,阐明不同水分条件下土壤中氮的产生、消耗、保存机制及其生态环境效应。结果表明: 土壤水分变化不影响草地和林地土壤氮初级矿化速率和铵态氮固定速率,水分含量由60% WHC增加至100% WHC后显著增加了林地土壤的初级硝化速率,但对草地土壤的初级硝化速率没有显著影响。60% WHC条件下草地和林地土壤的初级反硝化速率可以忽略不计,水分含量增加至100% WHC后土壤初级反硝化速率显著提高,且草地土壤的初级反硝化速率显著低于林地土壤。100% WHC条件下林地土壤初级硝化速率与铵态氮固定速率比值(gn/ia)和N₂O排放量均显著高于60% WHC;100% WHC条件下草地土壤的N₂O排放量显著高于60% WHC,但两个水分条件下的gn/ia值无显著差异。表明短期内水分含量的增加可能会增加草地和林地土壤氮转化的负面环境效应,且对林地土壤的影响尤为显著。