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.     

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.     

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.     

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.     

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.     

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     

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.     

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.     

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.     

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.     

A comparative study of dissolved organic carbon transport and stabilization in California forest and grassland soils

For soil carbon to be effectively sequestered beyond a timescale of a few decades, this carbon must become incorporated into passive reservoirs or greater depths, yet the actual mechanisms by which this occurs is at best poorly known. In this study, we quantified the magnitude of dissolved organic carbon (DOC) leaching and subsequent retention in soils of a coniferous forest and a coastal prairie ecosystem. Despite small annual losses of DOC relative to respiratory losses, DOC leaching plays a significant role in transporting C from surface horizons and stabilizing it within the mineral soil. We found that DOC movement into the mineral soil constitutes 22% of the annual C inputs below 40 cm in a coniferous forest, whereas only 2% of the C inputs below 20 cm in a prairie soil could be accounted for by this process. In line with these C input estimates, we calculated advective transport velocities of 1.05 and 0.45 mm year^?1 for the forested and prairie sites, respectively. Radiocarbon measurements of field-collected DOC interpreted with a basic transport-turnover model indicated that DOC which was transported and subsequently absorbed had a mean residence time of 90–150 years. Given these residence times, the process of DOC movement and retention is responsible for 20% of the total mineral soil C stock to 1 m in the forest soil and 9% in the prairie soil. These results provide quantitative data confirming differences in C cycles in forests and grasslands, and suggest the need for incorporating a better mechanistic understanding of soil C transport, storage and turnover processes into both local and regional C cycle models.     

A comparative study of dissolved organic carbon transport and stabilization in California forest and grassland soils

For soil carbon to be effectively sequestered beyond a timescale of a few decades, this carbon must become incorporated into passive reservoirs or greater depths, yet the actual mechanisms by which this occurs is at best poorly known. In this study, we quantified the magnitude of dissolved organic carbon (DOC) leaching and subsequent retention in soils of a coniferous forest and a coastal prairie ecosystem. Despite small annual losses of DOC relative to respiratory losses, DOC leaching plays a significant role in transporting C from surface horizons and stabilizing it within the mineral soil. We found that DOC movement into the mineral soil constitutes 22% of the annual C inputs below 40 cm in a coniferous forest, whereas only 2% of the C inputs below 20 cm in a prairie soil could be accounted for by this process. In line with these C input estimates, we calculated advective transport velocities of 1.05 and 0.45 mm year⁻¹ for the forested and prairie sites, respectively. Radiocarbon measurements of field-collected DOC interpreted with a basic transport-turnover model indicated that DOC which was transported and subsequently absorbed had a mean residence time of 90–150 years. Given these residence times, the process of DOC movement and retention is responsible for 20% of the total mineral soil C stock to 1 m in the forest soil and 9% in the prairie soil. These results provide quantitative data confirming differences in C cycles in forests and grasslands, and suggest the need for incorporating a better mechanistic understanding of soil C transport, storage and turnover processes into both local and regional C cycle models.     

Microbial communities and activities in alpine and subalpine soils

Soil samples were collected along two slopes (south and north) at subalpine (1500–1900 m, under closed vegetation, up to the forest line) and alpine altitudes (2300–2530, under scattered vegetation, above the forest line) in the Grossglockner mountain area (Austrian central Alps). Soils were analyzed for a number of properties, including physical and chemical soil properties, microbial activity and microbial communities that were investigated using culture-dependent (viable heterotrophic bacteria) and culture-independent methods (phospholipid fatty acid analysis, FISH). Alpine soils were characterized by significantly ( P <0.01) colder climate conditions, i.e. lower mean annual air and soil temperatures, more frost and ice days and higher precipitation, compared with subalpine soils. Microbial activity (soil dehydrogenase activity) decreased with altitude; however, dehydrogenase activity was better adapted to cold in alpine soils compared with subalpine soils, as shown by the lower apparent optimum temperature for activity (30 vs. 37 °C) and the significantly ( P <0.01–0.001) higher relative activity in the low-temperature range. With increasing altitude, i.e. in alpine soils, a significant ( P <0.05–0.01) increase in the relative amount of culturable psychrophilic heterotrophic bacteria, in the relative amount of the fungal population and in the relative amount of Gram-negative bacteria was found, which indicates shifts in microbial community composition with altitude.     

Diversity of dung-beetle community in declining Japanese subalpine forest caused by an increasing sika deer population

The Ohdaigahara subalpine plateau in Japan has recently suffered a reduction in primary forest land caused by an increasing population of sika deer (Cervus nippon). Deer have debarked many trees, causing dieback, gradually changing the primary forest first to light forest with a floor that is densely covered with sasa grass (Sasa nipponica) and then to S. nipponica grassland. To examine the effects of vegetative transformation on the dung-beetle community, we compared the diversity and abundance of dung-beetle assemblages in the primary forest, transition forest, and S. nipponica grassland using dung-baited pitfall traps. The species richness and species diversity (Shannon-Wiener index) were significantly highest in the primary forest and lowest in the S. nipponica grassland. The evenness (Smith-Wilson index) was highest in the primary forest and nearly equal in the transition forest and S. nipponica grassland. The abundance was apparently greater in the transition forest than in the primary forest and S. nipponica grassland. These results suggest that loss of primary forest resulting from an increasing deer population decreases the diversity of the dung-beetle community while increasing the abundance of dung beetles in the transition forest. Sika deer use transition forests and grasslands more frequently than primary forests as habitat, but an increase in dung supply there does not necessarily increase the diversity or abundance of dung-beetle assemblages.