Soil Community Composition Research Articles

Effect of Jhum Cycles on <i>Acidobacteria</i> and <i>Burkholderia</i> Community in the Rhizosphere of Mixed Crops of Different Jhum Fields

In the present study, culture-dependent and independent [Denaturing gradient gel electrophoresis (DGGE)] approach were used to analyze the effect of fallow cycle on bacterial populations associated with mixed crops selected from three different jhum fallow cycles (5-, 10- and 20- years) of Changki village, Nagaland. Two important bacterial phyla viz. Acidobacteria and Burkholderia were selected for DGGE analysis. According to the DGGE banding profile, Acidobacteria showed more richness compared Burkholderia. The presence and absence of few of the bands in the profile indicate the community shifts in the selected jhum fields. Shannon diversity index was higher in Acidobacteria than Burkholderia. Multivariate analysis showed that Acidobacteria community structure was similar among the crop plants of the same fallow cycle. Burkholderia community did not show clear separation among fallow cycles although crop of same fallow cycle tend to group together. ANOSIM and PERMANOVA showed significant differences in rhizosphere community pattern among fallow cycles and the crop plants of same fallow cycles indicated that both fallow cycle and crop plants are factors determining the Acidobacteria and Burkholderia community composition in jhum soils which was also confirmed by the culture-dependent analysis. Culturable bacterial counts were dependent on media used and significantly different at different fallow cycles. Bacterial communities (both culturable and DGGE patterns) were correlated with soil nutrients suggesting their importance in stability of jhum soil. The present study revealed that both fallow cycle and host plant may be the key factors in shaping many bacterial communities in jhum soils.

Environmental and plant community drivers of plant pathogen composition and richness.

Interactions between individual plant pathogens and their environment have been described many times. However, the relative contribution of different environmental parameters as controls of pathogen communities remains largely unknown. Here we investigate the importance of environmental factors, including geomorphology, climate, land use, soil and plant community composition, for a broad range of aboveground and belowground fungal, oomycete and bacterial plant pathogens. We found that plant community composition is the main driver of the composition and richness of plant pathogens after taking into account all other tested parameters, especially those related to climate and soil. In the face of future changes in climate and land use, our results suggest that changes in plant pathogen community composition and richness will primarily be mediated through changes in plant communities, rather than the direct effects of climate or soils.

Seasonal Changes in Soil Microbial Community and Co-Occurrence Network of Species of the Genus Corylus.

Hazelnut is one of the four major nuts in the world and has high nutritional and economic value. This study employed Illumina sequencing of ITS rDNA and 16S rRNA genes to identify the seasonal changes in soil microbial community, the predominant environmental factors driving microbial community composition, and the differences in soil microbial composition among different species of the genus Corylus. We found that the soil microbial community composition of species of Corylus changed significantly with the change in seasons. Corylus heterophylla and Corylus kweichowensis had more ectomycorrhiza in their soil compared to Corylus avellane. The main factor influencing fungal community composition in soil was the available potassium, while that of bacteria was the total phosphorus content. Co-occurrence network analysis revealed that the ratio of positive interaction to negative interaction in soil of C. heterophylla and Ping’ou (C. heterophylla × C. avellane) was higher, while the negative interaction of soil community structure in C. avellane was greater. The bacterial community was more stable than the fungal community according to microbial diversity and co-occurrence network analyses. The findings of this research may facilitate improvements to the production and soil system management in hazel planting processes.

Fate of antibiotic resistance genes in abandoned swine feedlots in China: seasonal variation

BackgroundEnvironmental hygiene concerns are needed to be settled before the reuse of abandoned swine feedlot sites. However, few researchers have focused on the fate of antibiotic resistance genes (ARGs) in soil microbiota around abandoned swine feedlots. In this study, we examined the seasonal alterations of ARGs and bacterial community composition in soil using quantitative PCR and high-throughput sequencing of 16S rRNA gene.ResultsThe seasonal variation patterns were different for different ARG subtypes and soil sampling sites. The bacterial community composition at the genus level generally showed no significant alteration from winter to summer. Moreover, the co-occurrence network suggested that the bacterial genera host range of ARGs was broader in the summer than in the winter.ConclusionThis study offers further data on ARG transfer risk in soil, emphasizing the necessity of continuous concern before land-reuse of abandoned feedlots.

Genome-resolved metagenomics reveals how soil bacterial communities respond to elevated H2 availability

Molecular hydrogen (H2) is a major energy source supporting bacterial growth and persistence in soil ecosystems. While recent studies have uncovered mediators of atmospheric H2 consumption, far less is understood about how soil microbial communities respond to elevated H2 levels produced through natural or anthropogenic processes. Here we performed microcosm experiments to resolve how microbial community composition, capabilities, and activities change in upland and wetland soils following H2 supplementation (at mixing doses from 0.5 to 50,000 ppmv). Genome-resolved metagenomic profiling revealed that these soils harbored diverse bacteria capable of using H2 as an electron donor for aerobic respiration (46 of the 196 MAGs from eight phyla) and carbon fixation (15 MAGs from three phyla). H2 stimulated the growth of several of these hydrogenotrophs in a dose-dependent manner, though the lineages stimulated differed between the soils; whereas actinobacterial lineages encoding group 2a [NiFe]-hydrogenases grew most in the upland soils (i.e. Mycobacteriaceae, Pseudonocardiaceae), proteobacterial lineages harboring group 1d [NiFe]-hydrogenases were most enriched in wetland soils (i.e. Burkholderiaceae). Hydrogen supplementation also influenced the abundance of various other genes associated with biogeochemical cycling and bioremediation pathways to varying extents between soils. Reflecting this, we observed an enrichment of a hydrogenotrophic Noviherbaspirillum MAG capable of biphenyl hydroxylation in the wetland soils and verified that H2 supplementation enhanced polychlorinated biphenyl (PCB) degradation in these soils, but not the upland soils. This study constitutes the first genome-resolved analysis of how soil microbial communities respond to elevated H2 availability. Overall, our findings suggest that soils harbour different hydrogenotrophic bacteria that rapidly grow following elevated H2 exposure. In turn, this adds to growing evidence of a large and robust soil H2 sink capable of counteracting growing anthropogenic emissions.

Influences of phosphorus and potassium deficiencies on the methanotrophic communities in rice rhizosphere

Soil methanotrophs can modulate net methane (CH4) emissions in rice paddy fields, but their growth and development depend, to a great extent, upon the soil nutrient status. In this study, a pot experiment was conducted to explore how deficiencies in soil phosphorus (P) or potassium (K) affect the methanotrophic abundance (based on pmoA q-PCR), community composition (based on MiSeq high-throughput sequencing) and CH4 oxidation potential using historically severe P and K deficient paddy soils, respectively. The results showed that P deficiency induced a significant decrease in methanotrophic abundance and potential activity in both rhizosphere and bulk soils. Additionally, P deficiency also caused clear shifts in the methanotrophic community composition within the rhizosphere, where the relative abundance of type II methanotrophs (e.g., Methylocystis and Methylosinus) increased while type I (e.g., Methylomonas, Methylobacter and Unclassified_typeIb) decreased. In contrast, K deficiency did not significantly affect the methanotrophic potential activity and community composition in both rhizosphere and bulk soils. More interestingly, P or K deficiency, particularly P deficiency, narrowed the differences in the abundance and community composition between rhizosphere and bulk soils, implying that P and K deficiencies could attenuate the rhizosphere effects on methanotrophic communities by limiting rice plant growth. Collectively, our results indicated that soil P deficiency, would inhibit soil CH4 oxidation directly or indirectly through restricting rice plant growth, while K deficiency have slight effects on the activity and community composition of soil methanotrophs.

Fungal Interactions Matter: Tricholoma matsutake Domination Affect Fungal Diversity and Function in Mountain Forest Soils.

Simple SummaryTricholoma matsutake forms a symbiotic association with hosts, developing mycelial aggregations, called ‘shiro’. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Here, we mainly aimed to study the fungal characteristics in the bulk soil (non-shiro) and shiro, using phospholipid fatty acids and illuninan sequencing in five habitats across landscapes in southwestern China. T. matsutake causes a lower fungal diversity and simplifies the fungal community composition in shiro soil compared with non-shiro soil across five forest types. We also found that geo-graphical proximity was accompanied by a similar fungal community structure but different contributions from specific species under five forest types. Among the co-existed fungi, Oidiodendron were found to collaborate with T. matsutake, whereas Helotiales and Mortierella showed a negative correlation with it. The selection of these taxa may be related to their ability to compete with resources and different nutrient strategists in the soil. Overall, we conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types.Tricholoma matsutake forms a symbiotic association with coniferous trees, developing mycelial aggregations, called ‘shiro’, which are characterized by distinct chemical and physical properties from nearby forest bulk soil. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Samples of shiro and non-shiro (nearby bulk soil) were taken from five field sites where sporocarps naturally formed. Phospholipid fatty acids (PLFA) and Illumina MiSeq sequencing were combined to identify fungal biomass and community structure. Matsutake dominated in the shiro, which had a significantly reduced saprotrophic fungi biomass compared to non-shiro soil. Fungal diversity was negatively correlated with the relative abundance of T. matsutake in the shiro soil. The fungal community in the shiro was characterized by similar fungal species composition in most samples regardless of forest types. Matsutake coexisted with a specific fungal community due to competition or nutrient interactions. Oidiodendron was positively correlated with the abundance of T. matsutake, commonly cohabitant in the shiro. In contrast, Helotiales and Mortierella were negatively correlated with T. matsutake, both of which commonly inhabit the non-shiro soil but do not occur in shiro soils. We conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types.

Response of soil bacterial community structure and function under two salt-tolerant plants in a coastal saline soil area of eastern Hebei province of China

The plants Feicai (Sedum aizoon L.) and dandelion(Taraxacum mongolicum Hand.-Mazz.) have good salt tolerance, and can improve soil quality and the micro-ecological environment. Coastal saline-soil plots planted with S. aizoon and T. mongolicum and bare plots were used to explore their effects on the microbial community structure of coastal saline soil. The diversity and function of soil bacterial communities were analyzed using Illumina MiSeq high-throughput sequencing technology. The results showed that the α-diversity of soil bacterial communities were higher in planted than in bare plots, in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The soil bacterial communities also changed after planting S. aizoon and T. mongolicum. The LDA effect size analysis showed that there were 37 indicator species among the three plot types. Correlation analysis of environmental factors showed that EC, AP, and OM were the main factors influencing bacterial community composition in this coastal saline soil. The PICRUSt functional prediction showed that the numbers of metabolic functions of bacterial communities were in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The results provide a theoretical basis and plant species for developing salt-tolerant bacterial resources and phytoremediation of coastal saline soil.

Impacts of experimental decreasing groundwater levels on bacterial community composition and hydrocarbon attenuation in oil-polluted soil from Northern China

Impacts of experimental decreasing groundwater levels on bacterial community composition and hydrocarbon attenuation in oil-polluted soil from Northern China

L-Canavanine, a Root Exudate From Hairy Vetch (Vicia villosa) Drastically Affecting the Soil Microbial Community and Metabolite Pathways.

L-Canavanine, a conditionally essential non-proteinogenic amino acid analog to L-arginine, plays important roles in cell division, wound healing, immune function, the release of hormones, and a precursor for the synthesis of nitric oxide (NO). In this report, we found that the L-canavanine is released into the soil from the roots of hairy vetch (Vicia villosa) and declines several weeks after growth, while it was absent in bulk proxy. Hairy vetch root was able to exudate L-canavanine in both pots and in vitro conditions in an agar-based medium. The content of the L-canavanine in pots and agar conditions was higher than the field condition. It was also observed that the addition of L-canavanine significantly altered the microbial community composition and diversity in soil. Firmicutes and Actinobacteria became more abundant in the soil after the application of L-canavanine. In contrast, Proteobacteria and Acidobacteria populations were decreased by higher L-canavanine concentration (500 nmol/g soil). Prediction of the soil metabolic pathways using PICRUSt2 estimated that the L-arginine degradation pathway was enriched 1.3-fold when L-canavanine was added to the soil. Results indicated that carbon metabolism-related pathways were altered and the degradation of nitrogen-rich compounds (i.e., amino acids) enriched. The findings of this research showed that secretion of the allelochemical L-canavanine from the root of hairy vetch may alter the soil microbial community and soil metabolite pathways to increase the survival chance of hairy vetch seedlings. This is the first report that L-canavanine acts as an allelochemical that affects the biodiversity of soil microbial community.

Multiple factors influence bacterial community diversity and composition in soils with rare earth element and heavy metal co-contamination

The effects of long-term rare earth element (REE) and heavy metal (HM) contamination on soil bacterial communities remains poorly understood. In this study, soil samples co-contaminated with REEs and HMs were collected from a rare-earth tailing dam. The bacterial community composition and diversity were analyzed through Illumina high-throughput sequencing with 16S rRNA gene amplicons. Bacterial community richness and diversity were lower in the co-contaminated soils than in the uncontaminated soils, with clearly different bacterial community compositions. The results showed that total organic carbon and available potassium were the most important factors affecting bacterial community richness and diversity, followed by the REE and HM contents. Although the canonical correspondence analysis results showed that an REE alone had no obvious effects on bacterial community structures, we found that the combined effects of soil physicochemical properties and REE and HM contents regulated bacterial community structure and composition. The effects of REEs and HMs on bacterial communities were similar, whereas their combined contributions were greater than the individual effects of REEs or HMs. Some bacterial taxa were worth noting. These specifically included the plant growth-promoting bacteria Exiguobacterium (sensitive to REEs and HMs) and oligotrophic microorganisms with metal tolerance (prevalent in contaminated soil); moreover, relative abundance of JTB255-Marine Benthic Group, Rhodobacteraceae, Erythrobacter, and Truepera may be correlated with REEs. This study was the first to investigate the responses of bacterial communities to REE and HM co-contamination. The current results have major implications for the ecological risk assessment of environments co-contaminated with REEs and HMs.

Responses of soil bacterial and fungal communities to the long-term monoculture of grapevine.

Soil microorganisms are essential for the long-term sustainability of agricultural ecosystems. However, continuous grapevine replanting can disrupt the stability of soil microbial communities. We investigated the bacterial and fungal abundance, diversity, and community composition in rhizosphere soils with continuous grapevine replanting for 5, 6, 7 (Y5, Y6, and Y7; short-term), and 20 (Y20; long-term) years with high-throughput sequencing. Results showed that diversities and abundances of bacterial and fungal communities in Y20 were significantly lower than in other samples. The bacterial and fungal community compositions were markedly affected by the replanting time and planting year. After short-term grapevine replanting, relative abundances of potential beneficial bacteria and harmful fungi in rhizosphere soils were higher compared to long-term planting. Bacterial and fungal communities were significantly correlated with available nitrogen (AN), available phosphorus, available potassium (AK), and pH. AK and AN were the primary soil factors related to the shift of bacterial and fungal communities. Bacterial and fungal co-occurrence patterns were remarkably affected by replanting time, showing that fallow land harbored co-occurrence networks more complex than those in other groups, with the Y20 group showing the lowest complexity. Then, we isolated the dominant fungi in grapevine rhizosphere soil after continuous replanting and verified the harmful effects of three candidate strains through pot experiments. The results showed that 12days post-treating the soil with fungal spore suspensions significantly inhibited grapevine seedlings' growth, whereas Fusarium solani inhibited plant growth. Overall, we showed that F. solani might be a potentially harmful fungus related to grapevine replant diseases. KEY POINTS: • Continuous grapevine planting reduced soil microbe diversities/abundances. • Beneficial bacteria and harmful fungi increased after short-term replanting. • F. solani may be a harmful fungus related to grapevine replant diseases.

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome.

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

Effects of Biogas Slurry Combined With Chemical Fertilizer on Soil Bacterial and Fungal Community Composition in a Paddy Field.

The application of biogas slurry and chemical fertilizer in paddy fields can be a practical method to reduce the environmental risk and utilize the nutrients of biogas slurry. The responses of bacterial and fungal communities to the application of biogas slurry and chemical fertilizer are important reflections of the quality of the ecological environment. In this study, based on a 3-year field experiment with different ratios of biogas slurry and chemical fertilizer (applying the same pure nitrogen amount), the Illumina MiSeq platform was used to investigate the bacterial and fungal community diversity and composition in paddy soil. Our results revealed that compared with the observations under regular chemical fertilization, on the basis of stable paddy yield, the application of biogas slurry combined with chemical fertilizer significantly enhanced the soil nutrient availability and bacterial community diversity and reduced the fungal community diversity. Dissolved organic carbon (DOC), DOC/SOC (soil organic carbon), available nitrogen (AN) and available phosphorus (AP) were positively correlated with the bacterial community diversity, but no soil property was significantly associated with the fungal community. The bacterial community was primarily driven by the application of biogas slurry combined with chemical fertilizer (40.78%), while the fungal community was almost equally affected by the addition of pure biogas slurry, chemical fertilizer and biogas slurry combined with chemical fertilizer (25.65–28.72%). Biogas slurry combined with chemical fertilizer significantly enriched Proteobacteria, Acidobacteria, Planctomycetes, Rokubacteria, and Ascomycota and depleted Chloroflexi, Bacteroidetes, Crenarchaeota, Basidiomycota, and Glomeromycota. The observation of the alteration of some bacteria- and fungus-specific taxa provides insights for the proper application of biogas slurry combined with chemical fertilizer, which has the potential to promote crop growth and inhibit pathogens.

Variations of earthworm gut bacterial community composition and metabolic functions in coastal upland soil along a 700-year reclamation chronosequence

Most ecosystem functions attributed to earthworms are mediated by their internal microbiomes, and these are sensitive to disturbances in the external environment. However, few studies have focused on the response of the earthworm gut microbiome to soil chronosequence. Here, we used 16S rRNA high-throughput sequencing and high-throughput quantitative PCR to investigate the variations in bacterial communities and functional gene abundance in earthworm (Lumbricina sp.) guts and upland soils under 700 years of cultivation. Our results indicated that 700 years of upland cultivation significantly shaped bacterial communities and increased functional traits of microbes in earthworm guts, which were more sensitive to cultivation age compared to the surrounding soils. The earthworm gut bacterial community changed rapidly over the first 300 years of cultivation and then changed slowly in the following centuries. Along with the cultivation age, we also observed that the earthworm gut microbiota was successive towards a copiotrophic strategy (e.g., Xanthobacteraceae, Nocardioidaceae, Hyphomicrobiaceae, and Bacillaceae) and higher potential functions (e.g., ureC, nirS, nosZ, phoD, and pqqC). Furthermore, canonical correspondence analysis further revealed that soil pH, C:N ratio, soil organic carbon, and total nitrogen were key abiotic drivers shaping earthworm gut bacterial communities. Taken together, this study reveals the succession of bacterial communities and potential functions in earthworm guts within 700 years of upland cultivation, which may provide a broader space for us to rationally exploit and utilize the interactions between soil and earthworm gut microbiotas to benefit the soil nutrient cycling process.

Herbivory and Soil Water Availability Induce Changes in Arbuscular Mycorrhizal Fungal Abundance and Composition.

We tested the prediction that abundance and composition of arbuscular mycorrhizal fungi (AMF) in Ipomopsis aggregata roots and soils are influenced by ungulate herbivory and drought conditions by examining the effects in a field setting over two years. We used a multi-metric approach to quantify AMF root colonization, AMF reproduction, and AMF community composition in roots and soils. We incorporated complimentary community characterization assays by morphologically identifying spores from trap cultures and the use of terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Herbivory caused a twofold increase in spore production, an increase in AMF taxa diversity in roots, and a shift in AMF species composition in rhizosphere soils. The impact of herbivory was dependent on water availability, which differed in the two contrasting years. This study demonstrates that both soil water availability and herbivory shape arbuscular mycorrhizal fungi communities. The changes to mycorrhizal communities may help in understanding mycorrhizal function in changing climates.

Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels

Parent materials and the fertility levels of paddy soils are highly variable in subtropical China. Bacterial diversity and community composition play pivotal roles in soil ecosystem processes and functions. However, the effects of parent material and fertility on bacterial diversity and community composition in paddy soils are unclear. The key soil factors driving the changes in bacterial diversity, community composition, and the specific bacterial species in soils that are derived from different parent materials and have differing fertility levels are unknown. Soil samples were collected from paddy fields in two areas with different parent materials (quaternary red clay or tertiary sandstone) and two levels of fertility (high or low). The variations in bacterial diversity indices and communities were evaluated by 454 pyrosequencing which targeted the V4–V5 region of the 16S rRNA gene. The effects of parent material and fertility on bacterial diversity and community composition were clarified by a two-way ANOVA and a two-way PERMANOVA. A principal coordinate analysis (PCoA), a redundancy analysis (RDA), and multivariate regression trees (MRT) were used to assess changes in the studied variables and identify the factors affecting bacterial community composition. Co-occurrence network analysis was performed to find correlations between bacterial genera and specific soil properties, and a statistical analysis of metagenomic profiles (STAMP) was used to determine bacterial genus abundance differences between the soil samples. The contributions made by parent material and soil fertility to changes in the bacterial diversity indices were comparable, but soil fertility accounted for a larger part of the shift in bacterial community composition than the parent material. Soil properties, especially soil texture, were strongly associated with bacterial diversity. The RDA showed that soil organic carbon (SOC) was the primary factor influencing bacterial community composition. A key threshold for SOC (25.5 g kg–1) separated low fertility soils from high fertility soils. The network analysis implied that bacterial interactions tended towards cooperation and that copiotrophic bacteria became dominant when the soil environment improved. The STAMP revealed that copiotrophic bacteria, such as Massilia and Rhodanobacter, were more abundant in the high fertility soils, while oligotrophic bacteria, such as Anaerolinea, were dominant in low fertility soils. The results showed that soil texture played a role in bacterial diversity, but nutrients, especially SOC, shaped bacterial community composition in paddy soils with different parent materials and fertility levels.

Predictors of soil fungal biomass and community composition in temperate mountainous forests in Central Europe

Fungi are a highly diverse group of soil organisms greatly contributing to the functioning of forest ecosystems. Consequently, the understanding of factors affecting their productivity and distribution is needed for the understanding of litter and soil ecology. While several drivers of fungal community composition have been identified, it is less clear how their relative importance depends on topsoil habitats and how consistent it is across fungal ecological guilds. Moreover, the predictors of fungal biomass are much less known than those of the community composition. To fill these knowledge gaps, we collected and analyzed a comprehensive dataset from a Central European coniferous forest, covering a broad range of elevations and vegetation types and spanning from managed forests to protected forests with minimal human intervention. Fungal standing biomass and composition (including root, soil and litter habitats) was analyzed in relation to site characteristics, soil and litter chemistry and vegetation (intense botanical surveys and molecular analysis of plant roots). We found that fungal biomass and community composition in soil were vertically stratified in our study area. The nutrient-rich litter contained elevated fungal biomass content and it was dominated by saprotrophic fungi, whereas bulk soil, with less fungal biomass, was dominated by ECM fungi and relatively depleted of saprotrophs. We show that vegetation was a key predictor of fungal community composition across all ecological guilds of fungi and habitats. pH of soil or litter was a significant predictor of fungal community composition in all studied habitats, whereas climatic (altitude) effects were observed for fungal biomass and composition in bulk soil. Finally, P was the most important nutrient in our study, explaining >20% of variance in fungal biomass and affecting fungal community composition across habitats. Our results support the idea that intense atmospheric deposition of N during last decades may have shifted Central European forests from N-limitation to P-limitation. In light of increased global anthropogenic N inputs projected for the next century, our results suggest that fungal productivity might become P-limited rather than N-limited in temperate forests.

Faster recovery of soil biodiversity in native species mixture than in Eucalyptus monoculture after 60years afforestation in tropical degraded coastal terraces.

Afforestation is an effective method to restore degraded land. Afforestation methods vary in their effects on ecosystem multifunctionality, but their effects on soil biodiversity have been largely overlooked. Here, we mapped the biodiversity and functioning of multiple soil organism groups resulting from diverse afforestation methods in tropical coastal terraces. Sixty years after afforestation from bare land (BL), plant species richness and the abundance of plant litter (398±85gm-2 ) and plant biomass (179±3.7tha-1 ) in native tree species mixtures (MF) were restored to the level of native forests (NF; 287±21gm-2 and 243.0±33tha-1 , respectively), while Eucalyptus monoculture (EP) only successfully restored the litter mass (388±43gm-2 ) to the level of NF. Soil fertility in EP and MF was increased but remained lower than in NF. For example, soil nitrogen and phosphorus concentrations in MF (1.2±0.2gkg-1 and 408±49mgkg-1 , respectively; p<0.05) were lower than in NF (1.8±0.2gkg-1 and 523±24mgkg-1 , respectively; p<0.05). Soil biodiversity, abundance (except for nematodes), and community composition in MF were similar or greater than those in NF. In contrast, restoration with EP only enhanced the diversity of microbes and mites to the level of NF, but not for other soil biota. Together, afforestation with native species mixtures can end up restoring vegetation and most aspects of the taxonomic and functional biodiversity in soil whereas monoculture using fast-growing non-native species cannot. Native species mixtures show a greater potential to reach completely similar levels of soil biodiversity in local natural forests if they are received some more decades of afforestation. Multifunctionality of soil biotic community should be considered to accelerate such processes in future restoration practices.

Biowaste compost amendment modifies soil biogeochemical cycles and microbial community according to aggregate classes

The use of biowaste compost as soil organic amendment is of great interest for soil recovery. However, there is little knowledge of detailed effects on chemical, microbial, and biochemical properties in different soil compartments (aggregate classes) following long-term amendment with biowaste compost. We studied the distribution of soil organic carbon (SOC), total nitrogen (TN), soil microbial biomass (SMB), microbial community composition and activity in bulk soils and in three water stable aggregate classes (>250, 250–53, and <53 μm), after seven years of different fertilization treatments: biowaste compost (Com), mineral NPK fertilizers (Min), biowaste compost with half-dose N fertilizer (ComN), and no fertilizers as control (Cnt). Microbial biomass was assessed through a double-stranded DNA (dsDNA) based method and enzyme activities were determined using a microplate-based fluorometric assay. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis was used to study the composition of both fungal and bacterial communities. Com and ComN treatments improved significantly SOC, TN and SMB in bulk soils and in all aggregate sizes. Composition of fungal and bacterial communities shifted with biowaste compost, more in soil aggregates than in bulk soils. To this change of microbial community composition in soil aggregates, corresponded a response of enzymes activities to fertilization treatments depending on aggregate size. Com treatment caused the highest enzyme activity in microaggregates (250–53 μm), whereas ComN and Min showed, in general, a higher activity in silt plus clay sized aggregates (<53 μm). The enzymes involved in biogeochemical cycle of P, with the exception of the phytase, displayed the lowest activity in macroaggregates (>250 μm), suggesting that the intensity of this cycle is lower in this soil niche; however, they increased with C accumulation due to both biowaste compost treatments. Furthermore, fungal diversity and richness decreased with fertilization treatments in all fraction except in macroaggregates. Thus, soil aggregates regulated the feedback of chemical, biochemical and microbial properties in response to soil fertilization strategies.