Soil Microbial Groups Research Articles

Using plant, microbe, and soil fauna traits to improve the predictive power of biogeochemical models

AbstractProcess‐based models describing biogeochemical cycling are crucial tools to understanding long‐term nutrient dynamics, especially in the context of perturbations, such as climate and land‐use change. Such models must effectively synthesize ecological processes and properties. For example, in terrestrial ecosystems, plants are the primary source of bioavailable carbon, but turnover rates of essential nutrients are contingent on interactions between plants and soil biota. Yet, biogeochemical models have traditionally considered plant and soil communities in broad terms. The next generation of models must consider how shifts in their diversity and composition affect ecosystem processes.One promising approach to synthesize plant and soil biodiversity and their interactions into models is to consider their diversity from a functional trait perspective. Plant traits, which include heritable chemical, physical, morphological and phenological characteristics, are increasingly being used to predict ecosystem processes at a range of scales, and to interpret biodiversity–ecosystem functional relationships. There is also emerging evidence that the traits of soil microbial and faunal communities can be correlated with ecosystem functions such as decomposition, nutrient cycling, and greenhouse gas production.Here, we draw on recent advances in measuring and using traits of different biota to predict ecosystem processes, and provide a new perspective as to how biotic traits can be integrated into biogeochemical models. We first describe an explicit trait‐based model framework that operates at small scales and uses direct measurements of ecosystem properties; second, an integrated approach that operates at medium scales and includes interactions between biogeochemical cycling and soil food webs; and third, an implicit trait‐based model framework that associates soil microbial and faunal functional groups with plant functional groups, and operates at the Earth‐system level. In each of these models, we identify opportunities for inclusion of traits from all three groups to reduce model uncertainty and improve understanding of biogeochemical cycles.These model frameworks will generate improved predictive capacity of how changes in biodiversity regulate biogeochemical cycles in terrestrial ecosystems. Further, they will assist in developing a new generation of process‐based models that include plant, microbial, and faunal traits and facilitate dialogue between empirical researchers and modellers.

Do biological legacies moderate the effects of forest harvesting on soil microbial community composition and soil respiration

Ecological forestry is a management approach that uses natural disturbance processes as models for designing silvicultural prescriptions that restore or sustain ecosystem biodiversity and function in actively managed forests. We evaluated how a novel ecologically-based multi-cohort silvicultural treatment affects the soil microbial community (SMC) and tested whether supplemental dead wood in the form of girdled trees alters these effects. We also tested SMC function by measuring soil CO2 flux over multiple growing seasons, and examined if these patterns were related to soil microbial groups. Our experimental harvests were conducted in second-growth northern hardwood forests in northern Wisconsin, USA. Treatments included a modified shelterwood harvest (SH), a shelterwood harvest plus dead wood supplementation (SH + CWD), and an unharvested control; here we report responses three to five years post-treatment. The SMC composition (determined using PLFA) in both harvests was significantly different from the control, a difference driven by greater bacterial abundance in the harvested areas, and particularly by gram negative bacteria in SH. Microbial community composition was not significantly different between the two harvests (SH and SH + CWD). Total soil respiration was significantly lower in SH than in the control and SH + CWD treatments, a difference most likely driven by a reduction of the autotrophic respiration component in SH treatments due to harvesting, while in the SH + CWD treatment roots from living girdled trees contributed to autotrophic soil respiration. The relationship between the SMC and soil respiration varied with treatment and season. In general, soil respiration in the unharvested controls was most significantly correlated with microbes that relate to autotrophic respiration sources, while respiration in SH + CWD was most significantly correlated with heterotrophic microbes. These results indicate that, although the SMC composition was affected by forest harvesting practices incorporating live and dead biological legacies, supplementing the number of standing dead trees through girdling and felling maintained SMC function, as measured through total soil respiration, an indicator of some important aspects of ecosystem function.

Elevated CO2 and warming cause interactive effects on soil carbon and shifts in carbon use by bacteria.

Accurate predictions of soil C feedbacks to climate change depend on an improved understanding of responses of soil C pools and C use by soil microbial groups. We assessed soil and microbial C in a 7-year manipulation of CO2 and warming in a semi-arid grassland. Continuous field isotopic labelling under elevated CO2 further allowed us to study the dynamics of the existing C (Old C) in soil and microbes as affected by warming. Warming reduced soil C under elevated CO2 but had no impact under ambient CO2 . Loss of soil C under warming and elevated CO2 was attributed to increased proportional loss of Old C. Warming also reduced the proportion of Old C in microbes, specifically the bacteria, but not the fungi. These findings highlight that warming impacts are C pool and microbial taxa dependent and demonstrate interactive effects of warming and atmospheric CO2 on soil C.

Short- and long-term warming alters soil microbial community and relates to soil traits

Climatic warming abnormally alters the structure and function of terrestrial ecosystems. It is vital to understand the response of belowground biota such as soil microbial communities to warming regimes, especially in native arid areas. The present in situ experiment was established to determine the effects of climatic warming regimes on soil microbe communities and the relationships between soil microbial groups and soil physicochemical features in a desert grassland ecosystem. Two warming regimes—long-term moderate warming (T1) and short-term acute warming (T2)—were established to simulate different climatic change scenarios. Soil from each plot was collected in 2014 at the late stage of the experiment, and phospholipid fatty acid (PLFA) profiling analysis was performed to assess the composition of the soil microbial communities. It was found that warming induced a severe water deficit stress. The T2 warming regime significantly increased the ratio of bacteria to fungi (B/F), and the ratio of Gram-positive to Gram-negative bacteria (GP/GN) in August. Belowground biomass (BGB) and soil organic carbon (SOC) were significantly correlated with all of the soil microbial groups in August. The changes in B/F and GP/GN ratios might indirectly induce changes in microbial structure. It was concluded that alterations in the structure of soil microbial communities may strongly depend on growing seasons and that soil nutrient status might have a profound impact on soil microbial communities’ responses to climatic warming.

Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area.

Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (Cmic); NO3-; NH4+; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil Cmic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil Cmic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil Cmic and soil fungal community structure were significantly related to levels of soil NO3-. Our analyses showed that even after 33years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil Cmic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil Cmic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.

Aggregate-related changes in soil microbial communities under different ameliorant applications in saline-sodic soils

Soil ameliorants can improve soil physico-chemical properties and activate microbial communities in saline-sodic soils. However, there has been less focus on how aggregate fractions affect soil microbial communities under different ameliorant applications. Here, we used the phospholipid fatty acid (PLFA) analysis to explore the effects of soil ameliorants on microbial communities within mega-aggregates (diameter of >2 mm, ME), macro-aggregates (diameter of 0.25–2 mm, MA), and micro-aggregates (diameter of <0.25 mm, MI), based on an 8-year rice (Oryza sativa L.) field experiment. The five treatments included CK, non-amended control; SS, amended with sandy soil; DG, amended with desulfurization gypsum; FM, amended with farm manure; and M, amended with a mixture of sandy soil, desulfurization gypsum, and farm manure. Relative to the CK treatment, the SS, DG, FM, and M treatments significantly decreased the soil pH and electrical conductivity and significantly increased the soil organic carbon (SOC) content of the MI, while the FM and M treatments also significantly improved the SOC content of the MA and ME. Irrespective of the ameliorant used, the absolute abundance of total PLFAs and most microbial groups generally varied with the SOC content as follows: MA > ME > MI. Meanwhile, the proportional abundance of arbuscular mycorrhizal fungi (AMF) varied between different aggregate fractions as follows: ME > MA > MI. Additionally, the DG treatment significantly enhanced the soil aggregate stability by increasing the AMF abundance, AMF/saprotrophic fungi ratio, and SOC content of the MI. Furthermore, soil microbial groups were highly correlated with soil SOC (P < 0.001), C/N ratio (P < 0.001), pH (P < 0.01), total nitrogen (P < 0.01), and the proportion of aggregates with a >0.25 mm diameter (P < 0.05). In conclusion, desulfurization gypsum is more effective for improving the properties of saline-sodic soils in the western Songnen Plain.

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China.

Microbially-mediated soil N mineralization and transformation are crucial to plant growth. However, changes in soil microbial groups and various N components are not clearly understood. To explore the relationship between soil N components and microbial communities, we conducted an in-situ experiment on two typically planted forest species, namely, Sibirica Apricot (SA) and Prunus davidiana Franch (PdF) by using closed-top polyvinyl chloride tubes. Changes in soil inorganic N, organic N (ON) fractions, and levels of microbial phospholipid fatty acids (PLFAs) were measured bimonthly from April 2012 to April 2013. Microbial PLFAs and the concentrations of easily-available microbial biomass N (MBN; ~60 mg kg-1), soluble ON (SON; ~20 mg kg-1), and inorganic N were similar between the two soils whereas the ON (~900 mg kg-1) and its major part total acid-hydrolyzable N (HTN; ~500 mg kg-1), were significantly different (p < 0.05) in most months (5/6 and 4/6; respectively). The canonical correlation analysis of soil N fractions and microbial parameters indicated that the relationship between total PLFAs (total biomass of living cells) and NH4+-N was the most representative. The relative contributions (indicated by the absolute value of canonical coefficient) of NH4+-N were the largest, followed by NO3−-N and MBN. For the HTN component, the relative percentage of hydrolyzable amino acid N and ammonium N decreased markedly in the first half of the year. Canonical variation mainly reflected the relationship between ammonium N and bacterial PLFAs, which were the most sensitive indicators related to soil N changes. The relative contributions of HTN components to the link between soil microbial groups and HTN components were ammonium N > amino acid N > amino sugar N. Observations from our study indicate the sensitivity of soil N mineralization indicators in relation to the temporal variation of soil microbial groups and N fractions.

Plant growth and oil contamination alter the diversity and composition of bacterial communities in agricultural soils across China

AbstractThe dynamics of microbial diversity in response to biotic and abiotic disturbances provide a sensitive indicator for evaluating the potential stability and degradation of soils in agro‐ecosystems. To determine the effect on soil bacterial communities of disturbances by plant growth (Robinia pseudoacacia) and oil contamination, we sequenced 16S rRNA genes using MiSeq technology. A greenhouse experiment was conducted using 21 agro‐soils from 19 provinces in China. Abiotic and biotic disturbances, including treating the soils with sterile water, crude oil, and/or an invasive plant, altered the bacterial community structure in the soils, increased bacterial richness, and reduced bacterial dispersion. Oil contamination exerted stronger effects on the bacterial α‐ and β‐diversity than plant growth. The different responses of bacterial communities and the core microbiome indicated that the disturbances shifted the prevalent soil microbial groups in agro‐ecosystems. Among different sampling sites, community dissimilarity increased with spatial distance. Edaphic factors (deterministic processes) exerted the primary influence on the assembly of soil microbiomes in agricultural fields, whereas geographic factors (stochastic processes) were less influential. The bacterial communities in agro‐soils from warmer regions were more sensitive to the disturbances. This study provides new insight into the alteration of soil microbiota by plant growth and oil contamination in agro‐ecosystems across a large spatial scale.

Concentration-dependent responses of soil bacterial, fungal and nitrifying communities to silver nano and micron particles.

The growing use of silver nanoparticles (AgNPs) is likely to result in increased environmental contamination. Although AgNPs have been reported to affect microbial communities in a range of ecosystems, there is still a lack of information concerning the effect of low concentrations of AgNPs on soil microbial community structures and functional groups involved in biogeochemical cycling. In this study, the concentration-dependent effects of AgNPs and silver micron particles (AgMPs) on bacterial and fungal community structures in an agricultural pastureland soil were examined in a microcosm-based experiment using enzyme analysis, molecular fingerprinting, qPCR and amplicon sequencing. Soil enzyme processes were impacted by Ag contamination, with soil dehydrogenase activity reduced by 1mgkg-1 of AgNPs and AgMPs. Soil urease activity was less susceptible, but was inhibited by ≥ 10mgkg-1 AgNPs. The significant (P ≤ 0.001) decrease in copy numbers of the amoA gene by 10mgkg-1 AgNPs indicated that archaea ammonia oxidisers may be more sensitive to AgNP contamination than bacteria. Amplicon sequencing revealed the bacterial phyla Acidobacteria and Verrucomicrobia to be highly sensitive to AgNP contamination. A broad reduction in the relative abundance of Acidobacterial genera was observed, with the exception of the genus Geothrix which increased in response to AgNP and AgMP amendment. Broad tolerance to Ag was observed among the Bacteriodetes, with higher relative abundance of most genera observed in the presence of AgNPs and AgMPs. The proteobacterial genus Dyella was highly tolerant to AgNPs and AgMPs and relative abundance of this genus increased with Ag concentration. Soil fungal community structure responded to both AgNPs and AgMPs, but the nanoparticle had an impact at a lower concentration. This study demonstrates that pastureland soil microbial communities are highly sensitive to AgNP amendment and key functional processes may be disrupted by relatively low levels of contamination.

Microbial responses to temperature sensitivity of soil respiration in a dry fallow cover cropping and submerged rice mono-cropping system

Soil heterotrophic respiration (SHR) increases exponentially with temperature and this general information has been incorporated into soil carbon models. However, the positive feedback of warming to SHR remains uncertain, mostly due to the differential response of soil microbial community to warming under dry and flooded conditions in a rice mono-cropping system. In this study, we aimed to evaluate the relationship between SHR and microbial functional groups during the fallow and flooded rice cultivation seasons under changing temperature in a rice mono-cropping system. Field experiments were conducted to investigate SHR, soil microbial functional groups and biomass, and temperature sensitivity of SHR (Q10) under dry fallow conditions during the cover cropping season and under flooded conditions during the rice cropping season. We found that SHR increased with increasing air and soil temperature, carbon availability, and soil microbial community composition and biomass in the fallow season, whereas a decrease in SHR in spite of an increase in temperature and carbon availability was observed under flooded conditions during the rice cropping season. Furthermore, a nonlinear response of microbial community composition and biomass with SHR was noticed during the flooded rice cropping season. This suggests that flooding could be the limiting factor for temperature sensitivity of SHR as well as microbial community composition in a rice mono-cropping system. Flooding the soil significantly (p < 0.01) decreased Q10. We therefore conclude that temperature, moisture region and carbon availability, rather than only soil microbial community composition are responsible for the spatiotemporal variation in SHR in a rice mono-cropping system in this region.

Effects of trifluralin on the soil microbial community and functional groups involved in nitrogen cycling

Large amounts of trifluralin are applied each year for weed control; however, its effects on soil microbial communities and functions are unknown. Two agricultural soils, one silty loam and one silty clay were spiked with TFL (0, 0.84, 8.4, and 84 mg kg–1) and studied the effects using a laboratory microcosm approach. The half-lives were 44.19–61.83 d in all cases. Bacterial abundance increased 1.12–5.56 times by TFL, but the diversity decreased. From the next-generation sequencing results, TFL altered the bacterial community structure, which initially diverged from the control community structure, then recovered, and then diverged again. Linear discriminant analysis effect size indicated that Sphingomonas and Xanthomonadaceae were the predominant species on day 7 and 15 in TFL treatments. N2-fixing bacteria were initially increased, then decreased, and then recovered, and it was positively correlated with NH4+-N content. Compared with the control, ammonia-oxidizing bacteria were decreased by 25.51–92.63%, ammonia-oxidizing archaea were decreased by 17.12–85.21% (except day 7), and the NO3−-N concentration was also inhibited. In contrast to bacteria, fungal abundance was inhibited without any observable effects on fungal diversity or community structure. These results suggest that TFL impacts soil bacterial community and alters functional microorganisms involved in soil N processing.

Effect of Liquid Digestate on Agricultural Soil-II: Microbial Population Dynamics

The aim of this study was to investigate the effect of liquid digestate (produced from anaerobic digestion of organic municipal solid waste) on the population dynamics of selected soil microbial groups during cultivation of maize plants. Maize seeds where subjected to various concentrations (between 0% to 72%) of the digestate with a total of ten (10) runs. One set of experimental runs were treated with one-time application of the corresponding digestate concentration (OTDA). Another set of experimental runs were treated with two-time application of the corresponding digestate concentration (TTDA). The first application of the digestate (for OTDA and TTDA) was conducted two weeks after sowing while the second application (for TTDA alone) was conducted three weeks after the first application. During the growth of maize plants, the populations of soil aerobic bacteria (AEB), strict anaerobic bacteria (SAB), ammonia oxidizing bacteria (AOB), nitrate reducing bacteria (NRB) and fungi (FUN) where monitored using standard cultural methods. In OTDA and TTDA treatments, the population of soil AEB, SAB, AOB, NRB and FUN ranged from 3.0 × 106 CFU/g to 50.2 × 106 CFU/g and 3.1 × 106 CFU/g to 78.6 × 106 CFU/g; 1.9 × 104 CFU/g to 7.2 × 105 CFU/g and 2.2 × 104 CFU/g to 2.53 × 105 CFU/g; 0MPN/g to 4.3 × 104 MPN/g and 0MPN/g to 3.9 × 105 MPN/g; 0 MPN/g to 4.4 × 105 MPN/g and 0 MPN/g to 1.4 × 105 MPN/g and 1.3 × 103 CFU/g to 2.6 × 104 CFU/g and 1.2 ×103 CFU/g to 9.4 × 103 CFU/g respectively before and 70 days after applying the digestate. Bacteria species isolated appear to belong to genera such as Arthrobacter, Azotobacter, Flavobacterium, Nocardia, Bacillus, Clostridium, Cellulomonas, Micrococcus and Pseudomonas. Fungi species isolated appear to belong to genera such as Aspergillus, Cladosporium, Fusarium, Geotrichum, Penicillium, Rhizopus and Trichoderma. Digestate application appears to have increased the population of soil microbes with time during the cultivation of maize plants.

The interaction of soil phototrophs and fungi with pH and their impact on soil CO2, CO18O and OCS exchange

The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (OCS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (α, β and γ) may have different affinities to CO2 and OCS and their expression should also vary between different microbial groups, differences in the community structure could impact the ‘community-integrated’ CA activity differently for CO2 and OCS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and OCS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototrophs. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototrophs abundance. OCS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. Our findings demonstrate that soil-atmosphere CO2, OCS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and supports the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and OCS.

Determinants of native and non‐native plant community structure on an oceanic island

AbstractUnderstanding the relative importance of environmental and anthropogenic factors in driving plant community structure, including relative dominance of native and non‐native species, helps predict community responses to biological invasions. To assess factors influencing plant communities on San Clemente Island, USA, we conducted an islandwide vegetation survey in which we measured plant species richness and percent cover of native and non‐native plants, as well as physical environmental variables, soil chemical properties, abundance of soil microbial functional groups (e.g., arbuscular mycorrhizal fungi [AMF]), and a human disturbance variable (distance to road). We found that total plant species richness decreased with increasing non‐native plant cover, soil pH, and AMF abundance. Native plant cover increased with increasing distance to a major paved road and decreased with increasing soil moisture and pH. Non‐native plant cover decreased with increasing distance to a major paved road and increased with increasing soil moisture, AMF abundance, and from southwest to northeast, a geographic/climatic gradient that represents increasing moisture. Nonmetric multidimensional scaling ordination further illustrated that trends in plant community composition were correlated with elevation, distance to a major paved road, and soil moisture, organic matter, and ammonium. These results suggest complex effects of physical environmental, soil chemical, and human‐related factors on plant community structure on an oceanic island, and moreover, that different factors affect cover of native and non‐native plants. Notably, our observation of apparent moisture limitation of non‐native plants suggests that, in some contexts, drought conditions can limit plant invasions and may even represent an opportunity for efficient control or eradication of invasive plants. The apparent negative effect of non‐native plants on native plant cover and overall plant species richness represents a conservation concern for native biodiversity on oceanic islands and suggests the potential for community reassembly as invasive species increasingly dominate due to anthropogenic disturbances.

Long-term biosolids application alters the composition of soil microbial groups and nutrient status in a pine plantation

Tree nutrient concentrations, root biomass, soil nitrogen (N) and phosphorus (P) contents, and enzyme activities were determined in a radiata pine plantation (Pinus radiata D. Don) on a sandy loam soil receiving 19 years of repeated biosolids applications, and the composition of soil microbial groups was assessed using phospholipid fatty acid analysis. Biosolids application significantly increased soil organic N, available P and foliar N concentration, but had no significant impact on foliar P concentration over the long term. Biosolids application improved aboveground tree growth but reduced fine-root biomass. Repeated biosolids applications also altered the composition of soil microbial community and increased the potential activities of N-acetyl-β-glucosaminidase and acid phosphomonoesterase. Changes in soil N and P availability were better explained by variations in the composition of bacterial groups than those of fungal groups. The fungi-to-bacteria ratios were not changed, but arbuscular mycorrhizal fungi were suppressed possibly due to elevated soil P caused by biosolids application. The ratios of Gram-positive to Gram-negative bacteria were significantly increased by biosolids application and were linked to increased N mineralisation rates. In addition, it is evident that variations in soil P availability and the composition of soil microbial groups following biosolids application were not significantly related to foliar P status. These findings contribute to a better understanding of the effects of biosolids application on microbial-mediated soil N and P processes.

Soil microorganisms at the windthrow plots: the effect of post-disturbance management and the time since disturbance

Abstract: Wind disturbance is a major natural driver of forest dynamics in a large part of Europe and can affect soil properties in different ways and for different time. The present study focuses on the effects of post-disturbance management of windthrow plots in the Tatra Mountains, Slovakia, on soil microorganisms ten years after the disturbance. Their comparison with the microbial characteristics at a new windthrow plot caused by strong wind in 2014 was also carried out. Three research plots differing in the way of their management after the windstorm in 2004 (EXT, salvage plot; FIR, salvage plot affected by fire; NEX, unsalvaged plot) and the plot destroyed by strong wind in May 2014 (REX) were used for study. Ten soil samples were taken from the mineral A-horizon (depth: 0-10 cm) at each plot in autumn 2014. In soil samples, soil chemical and microbial characteristics (microbial biomass C, basal and substrate-induced respiration, N-mineralisation, catalase activity, richness and diversity of soil microbial functional groups based on the Biolog approach) were determined. Ten years after the disturbance we still observed significant differences in microbial characteristics between FIR and the other plots, with higher microbial activity at the FIR, while no significant differences were found among the other plots. The results indicate that at a higher altitude the effect of fire on soil microorganisms is more distinct than removing or not removing of fallen trees and persists even over a decade.

Soil Microbial Communities in Natural and Managed Cloud Montane Forests

Forest management often results in changes in soil microbial communities. To understand how forest management can change microbial communities, we studied soil microbial abundance and community structure in a natural Chamaecyparis (NCP) forest, a disturbed Chamaecyparis (DCP) forest, a secondary (regenerated) Chamaecyparis (SCP) forest and a secondary (reforested) Cryptomeria (SCD) forest. We analyzed soil microbial abundance by measuring phospholipid fatty acids (PLFAs) and microbial community structure by denaturing gradient gel electrophoresis (DGGE) in the studied forest soils. The content of the soil PLFA fungal biomarker decreased from NCP to SCP, DCP and SCD forest soils, associated with the degree of disturbance of forest management. The ratio of soil Gram positive–to-negative bacteria and the stress index (16:1ω7t to 16:1ω7c) increased from NCP to SCP and DCP soils; thus, disturbed forests except for SCD showed increased soil microbial stress. Principal component analysis of soil microbial groups by PLFAs separated the four forest soils into three clusters: NCP, DCP and SCP, and SCD soil. The DGGE analysis showed no difference in the microbial community structure for NCP, DCP and SCP soils, but the community structure differed between SCD and the three other forest soils. In cloud montane forests, disturbance due to forest management had only a slight influence on the soil microbial community, whereas reforestation with different species largely changed the soil microbial community structure.

Microbial community and associated enzymes activity influence soil carbon chemical composition in Eucalyptus urophylla plantation with mixing N2-fixing species in subtropical China

Background and aims Microbial communities and their associated enzyme activities affect the quantity and chemical quality of carbon in soil. We aimed to evaluate the biochemical mechanisms underlying how N2-fixing species influences soil organic carbon chemical composition through soil microbial functional groups and enzyme activities.

Arbuscular mycorrhizal fungal assemblages in biological crusts from a Neotropical savanna are not related to the dominant perennial Trachypogon

Knowledge of the arbuscular mycorrhizal fungal assemblages in the Trachypogon savanna ecosystems is very important to a better understanding of the ecological processes mediated by this soil microbial group that affects multiple ecosystem functions. Considering the hypothesis that the biocrusts can be linked to vegetation through the arbuscular fungi mycelial network, the objectives proposed in this study were to determine (i) whether there are arbuscular mycorrhizal fungi (AMF) in the biocrusts (ii) whether arbuscular mycorrhizal fungal assemblages are linked to the Trachypogon patches, and (iii) whether the composition of the assemblages is related to soil properties affected by microbiological activity. The community structure of the AMF was investigated in three habitats: rhizospheric soil and roots of Trachypogon vestitus, biological soil crusts, and bare soil. The canonical correspondence analysis showed that two soil properties related to enzymatic activity (protease and β-glucosidase) significantly affected the community composition of the AMF. The biocrusts in the Venezuelan savanna are colonized by an AM fungal community linked to that of the bare soil and significantly different from that hosted by the roots of the surrounding T. vestitus, suggesting that assemblages of AMF in biocrusts might be related more closely to those of annual plant species appearing in favorable conditions.

Browsing by an invasive herbivore promotes development of plant and soil communities during primary succession

Summary Invasive herbivores can strongly affect ecosystems by reducing or removing native plant species, and early in primary successions they could have enduring consequences for plant community assembly and ecosystem functioning, although this has seldom been explored. Invasive brushtail possums (Trichosurus vulpecula) browse from ground levels to forest canopies in New Zealand, including on plant species common early in primary succession. We used exclosures (fenced on the top as well as the sides) and corresponding control plots to study effects of brushtail possums on primary successions on bare landslide surfaces in the South Island of New Zealand. We then conducted repeated measurements of the plant community over 11 years and at the end also quantified soil abiotic and biotic properties. Above‐ground, plant biomass increased from close to zero to &gt; 1000 g dry mass m−2 after 11 years in both exclosures and control plots, with significantly more biomass of the N2‐fixing tree Carmichaelia odorata in the controls. Brushtail possums reduced the biomass in the control plots of small‐stature grasses and sedges in the first 3 years. Plant species richness was greater in control than exclosure plots throughout the experiment. Below‐ground, soil carbon and nitrogen concentrations and the biomass of all major soil microbial groups were significantly greater in the control than exclosure plots, although soil nematode abundances were not. Below‐ground effects could be attributed to the greater biomass of Carmichaelia in control plots. Synthesis. Our study shows that an invasive herbivore exerted strong effects on the rate and trajectory of primary succession by altering plant community assembly. Herbivore exclusion resulted in reduced biomass of a key N2‐fixing tree that drives forest development, with important below‐ground consequences. These results support a view that restoration of ecosystems needs to consider the consequences of altering plant community structure before removing invasive herbivores.