查看更多>>摘要：? 2022 The AuthorsSoil ecology is witnessing exponential growth in the number of studies using co-occurrence network analysis. Researchers reconstruct networks based on the co-occurrence of taxa or genes across soil samples at a wide range of geographic scales - from single aggregates to the whole planet - and taxonomic scopes, some studies targeting specific taxa or guilds to others surveying the whole microbiome as well as micro- and mesofauna. Co-occurrence networks can be very useful to extract simple patterns from complex datasets. Applications include the detection of abiotic and biotic factors that determine community structure, the identification of keystone taxa and their relationship to specific soil functions, and the inference of mechanisms of community assembly. However, networks are more and more often misused and serve as mere graphic tools with no attempt at hypothesis testing. In this perspectives article, we first review the main usage of co-occurrence network analysis in soil ecology during the last decade. We then discuss the applications and caveats of network analysis in soil ecology, leaving apart strictly methodological aspects of network reconstruction, which is beyond the focus of this article. Finally, we include recommendation guidelines – such as the possibility of informing networks with geographic, environmental and/or phylogenetic information – with the hope that this will facilitate network analysis to become a useful tool that helps elucidate meaningful patterns in soil ecology.
查看更多>>摘要：? 2022Nitrous oxide (N2O) production in tropical soils cultivated with sugarcane is associated with ammonia-oxidizing bacteria (AOB) and fungal denitrifiers. However, the taxonomic identities and the community diversities, compositions, and structures of AOB and fungal denitrifiers in these soils are not known. Here, we examined the effects of applying different concentrations of an organic recycled residue (vinasse: regular non-concentrated or 5.8-fold concentrated) on the dynamics of AOB and fungal denitrifier community diversity and composition and greenhouse gas emissions during the sugarcane cycle in two different seasons, rainy and dry. DNA was extracted from soil samples collected at six timepoints to determine the dynamics of amoA-AOB and nirK-fungal community diversity and composition by amplicon sequencing with gene-specific primers. Bacterial and archaeal amoA, fungal and bacterial nirK, bacterial nirS and nosZ, total bacteria (16S rRNA) and total fungi (18S rRNA) were quantified by real-time PCR, and N2O and CO2 emissions were measured. The genes amoA-AOB and bacterial nirK clade II correlated with N2O emissions, followed by fungal nirK. The application of inorganic nitrogen fertilizer combined with organic residue, regardless of concentration, did not affect the diversity and structure of the AOB and fungal denitrifier communities but increased their abundances and N2O emissions. Nitrosospira sp. was the dominant AOB, while unclassified fungi were the dominant fungal denitrifiers. Furthermore, the community structures of AOB and fungal denitrifiers were affected by season, with dominance of uncultured Nitrosospira and unclassified fungi in the rainy season and the genera Nitrosospira and Chaetomium in the dry season. Nitrosospira, Chaetomium, Talaromyces purpureogenus, and Fusarium seemed to be the main genera governing N2O production in the studied tropical soils. These results highlight the importance of deciphering the main players in N2O production and demonstrate the impact of fertilization on soil microbial N functions.
查看更多>>摘要：? 2022 Elsevier LtdSoil inoculation from plant species-rich into species-poor grasslands may enable the establishment of self-facilitating networks between microbes and vegetation, thereby steering ecosystem development. We conducted a three-year experiment that covered a wide range of post-agricultural grasslands to determine how succession is affected by the interactive effects of edaphic properties, grass layer removal and hay or soil fragment transfer from a late-successional donor grassland. Soil inoculation generally impacted community assembly of vegetation and fungi, but not of prokaryotes. Effects were strongest when preceded by removal of the grass layer, indicating the importance of priority effects and dispersal limitation. Inoculation enabled the establishment of putative rhizosphere-associated fungal taxa, particularly from the families Helotiaceae, Glomeraceae and Archaeorhizomycetaceae. Nonetheless, effect sizes were mostly small, as was overall resemblance of the receptor grasslands to the donor. Fungal communities were primarily shaped by environmental filters and only reached a high resemblance to the donor in nutrient-poor sites. Shifts in the vegetation were strongest in those grasslands where the mycobiome more closely resembled that of the donor. Soil inoculation generally facilitates colonization by target plant and fungal communities, where establishment success of the former can be predicted by the latter, but the final outcome of succession is environmentally determined.
查看更多>>摘要：? 2022 Elsevier LtdClimatic variability along elevational gradients affects biodiversity and produces a natural range of conditions for realistic experiments. Soil biodiversity is expected to respond to the general climatic conditions, as well as microclimatic effects. With the Illumina MiSeq high-throughput sequencing technique, we systematically examined the taxonomic and phylogenetic diversity of soil bacteria and fungi along a 320-1350 m elevational gradient in subtropical forests. Microclimate data under continuous in-situ monitoring, soil physicochemical properties, and plant composition attributes were collected in the forest sites. We found a contrasting pattern in soil bacterial and fungal taxonomic diversity, with monotonically decreasing bacteria populations and no obvious change in fungi taxonomic richness but increased Shannon-Wiener index with increasing elevation. However, the analysis of the richness-dependent phylogenetic index showed no bacterial phylogenetic variability across the elevation gradient, whereas fungal phylogenetic variability increased with greater elevation. Soil temperature and pH were strongly associated with bacterial diversity, but less well correlated with fungal diversity. Microbial community structure differed taxonomically and phylogenetically along the elevation gradient and was most strongly related to soil temperature, followed by soil variables such as soil pH and N content. We conclude that microclimates are ecologically significant in mediating soil microbial community assembly.
查看更多>>摘要：? 2022 Elsevier LtdPlant community composition can alter soil microbial community structure and function, and further influence the process of soil N transformation. However, this effect is rarely noticed in forest types characterized by understory vegetation, especially in N-limited boreal forests where the understory vegetation substantially contributes to soil nutrient cycling. To investigate whether forest types characterized by understory vegetation can affect soil N mineralization and bacterial community, we determined mineral N contents, net N mineralization rates, soil bacterial community and microbial biomass in soils under three types of larch forest (Sphagnum-Bryum-Rhododendron tomentosum (previously: Ledum palustre)-Larix gmelinii forest(SLL), Rhododendron dauricum-Larix gmelinii forest (RL), and Rhododendron tomentosum-Larix gmelinii forest (LL)) in the typical boreal climatic region in northeast China. We found that soil N availability, soil N mineralization rates, soil bacterial community and microbial biomass vary with the difference of the understory vegetation, and these changes were stronger in the 0–10 cm soil layer than in the 10–20 cm soil layer. In addition, compared with soil N content, soil microbial biomass was more strongly correlated with soil N mineralization. Structural equation modeling was used to analyze the effects of driving factors and pathways on soil N dynamics. The results suggested that soil N mineralization was related to forest type and soil microbial biomass, while soil microbial biomass was significantly affected by soil bacterial composition. Finally, abundances of Actinobacteria, Patescibacteria and Chloroflexi were significantly correlated with soil N mineralization. Together, these mechanisms provide insight into the important function of understory vegetation in the process of soil N cycling in the boreal region.
查看更多>>摘要：? 2021Nitrogen (N) deposition poses a threat to terrestrial biodiversity and ecosystem functioning globally. However, little is known concerning how the structure and function of litter fauna communities will respond in this context. Here, a gradient of N deposition (0, 20, and 40 kg N ha?1 yr?1) was simulated in a subtropical forest of southwestern China, to assess the potential effects of increased N deposition on the trophic structure and functioning of fauna communities in decomposing leaf litters of three main subtropical plant functional groups covering a total of 18 species: six evergreen broadleaf, six deciduous broadleaf, and six coniferous trees. We found that N addition shifted the trophic structure of fauna communities in decomposing litter, and different fauna feeding guilds showed distinct response patterns. Specifically, N addition increased the abundance of predators, decreased the abundance of omnivores, while detritivores were less affected. Compared to deciduous broadleaf and coniferous litters, evergreen broadleaf litter had less complex structure of fauna communities, but it decomposed slower. Further, structural equation modeling (SEM) showed that N addition increased litter decomposition in part via changing the trophic structure of fauna communities, with a positive correlation between predators and detritivores being associated with higher decomposition. As omnivores often exhibit top-down pressure on all other trophic guilds in (sub-)tropics, our observed shifts in trophic structure and litter decomposition might be partly due to the N addition-induced declines in omnivorous ant population. Future studies should investigate the role of bottom-up and top-down forces between detritivores, predators, and omnivores in driving litter decomposition. Collectively, our findings suggest that (i) N deposition consistently shifts the trophic structure of fauna communities across litter types, and (ii) such a shift further translate into changes in the functioning of subtropical forest ecosystems.
查看更多>>摘要：? 2022 The AuthorsCapturing the complexity of soil life for soil quality assessments is one of the most challenging paradoxes of contemporary soil science. Soil biota perform a plethora of processes that are fundamental to soil quality. As the concept of soil quality developed, so have the attempts to integrate soil biological measurements into monitoring schemes from field to regional scale. To date, however, soil science has not yet succeeded to provide flexible yet objective biological indicator methods to assess soil multifunctionality, customised to the user's context. We present an integrative framework and elucidate the who and how of soil multifunctionality. The framework encompasses the current scientific understanding of the role of soil biota in supporting the many soil processes that underly soil quality. We specified these relationships for four soil functions (Carbon and Climate Regulation, Water Regulation and Purification, Nutrient Cycling, and Disease and Pest Regulation). We identify challenges often encountered in soil quality assessment and monitoring schemes and discuss how the framework can be applied to provide a flexible selection tool. Soil quality assessments are conducted in different contexts. As assessment objectives range from mechanistic understanding, to functional land management and large spatial scale monitoring so will the practical and logistical constraints for method selection vary. Biological assessments need to move beyond the quest for a one-size-fits-all minimum dataset, and adopt a more nuanced selection approach founded in soil biology. We stress that biological attributes should not be considered in isolation but alongside soil chemical and physical attributes, as well as management and environmental contextualisation. The presented framework offers a structure to further quantify, understand and communicate the who and how of soil biology in defining multifunctionality.
查看更多>>摘要：? 2021 Elsevier LtdRed wood ants are ecologically important species in Europe that form large colonies. Their nest mounds are characterized by stable microclimatic conditions, that are favourable to the development of rich invertebrate and microbial communities. Through their respiration processes, all these inhabitants contribute to the total gas emissions of the mounds. Quantifications of red wood ant mounds CO2 production are only available from Northern and Central Europe, and the Alps, where these ants are common. During the second half of the last century some species were transplanted from the Alps to southernmost sites, where they were not present, to be employed as biocontrol agents. No information on the contribution of these low-latitudes populations to the local forest CO2 production is available. The microbial communities living within red wood ant mounds are also poorly known. In this study, we investigated the CO2 gas emissions and the microbiome of the mounds of an introduced population of the red wood ant Formica paralugubris in a Southern Europe montane forest. We found that ant mounds produced more CO2 than the forest soil, and that their CO2 efflux as well as internal concentration were higher during summer than winter, with a lighter CO2 carbon isotopic signature in summer than winter, likely due to an increased ant activity. Moreover, the top part of the mound was characterised by higher CO2 efflux and lower CO2 internal concentration compared to the bottom, probably due to its internal structure and conditions. The isotopic signature of the mound material was similar between summer and winter, suggesting a metabolic similarity of the microbial communities. Also, we estimated the ants’ relative contribution to the total mound CO2 production to be 83%, whereas the microbiota CO2 contribution was estimated at 17%. Finally, the mound microbiome composition varied between summer and winter, though no seasonal difference in the diversity indexes or β-diversity was found. Our results demonstrate the impacts of the introduced red wood ants on the carbon dynamics of the recipient ecosystem.
查看更多>>摘要：? 2021Soil denitrification produces the potent greenhouse gas and ozone depleter nitrous oxide (N2O). We previously linked soil N2O emission potential (N2O/N2O + N2) to a continuum of denitrification phenotypes in 20 pasture soils but were unable to determine their proximal cause. At one end of the continuum, soils carried out completely concurrent production and reduction of N2O (concurrent phenotype) while at the other end soils delayed N2O reduction until almost all added nitrate (NO3?) was accumulated as N2O (sequential phenotype). In an unsealed environment, the later phenotype is predicted to emit most added N as N2O. Here we tested the role of delayed N2O reductase synthesis and nitrite (NO2?) based impairment of N2O reduction as determinants of delayed N2O reduction in soils with sequential phenotypes. Nitric oxide (NO), N2O and N2 accumulation were measured in response to added NO3?, NO2? and N2O in anoxic batch incubations of fresh or pre-incubated soil using automated gas chromatography. Successive NO3? additions drove 6 of 7 soils towards increasingly concurrent N2O production/reduction, suggesting delayed production of N2O reductase may be the cause of delayed N2O reduction in initially sequentially denitrifying soils. NO2? addition (2 mM NO3? + 1 mM NO2? vs. 3 mM NO3? control) to sequentially and concurrently denitrifying soil demonstrated that NO2? impairs N2O reduction, even when N2O reductase was fully induced (pre-incubated soils, 1 mM NO2? + 42 μmol N2O vs. 42 μmol N2O control). Further, 2 pieces of evidence suggest that differences in NO2? accumulation are a probable cause of the previously observed denitrification phenotypes. 1) 48 fold higher NO2? accumulation in the sequential vs. concurrent soil in response to 3 mM NO3? addition. 2) the concurrent timing of NO2? depletion/N2O reduction in the sequential soil. However, these observations should be confirmed in a greater number of soils. Inhibition of N2O reductase by NO is proposed as a potential proximal cause of impaired early N2O reduction which could link separate effectors (NO2?, carbon, successive NO3? additions) to a common inhibitory mechanism.
查看更多>>摘要：? 2022 Elsevier LtdThe loss of tree health is a global concern with many unknown cascading impacts on the diversity and function of forest ecosystems. Specifically, it is uncertain how the process of tree decline and mortality driven by exotic pathogens might alter the soil microbiome. Here we combined high-throughput sequencing, neighborhood models, and network analysis to explore the impacts of the decline of a Mediterranean tree species, Quercus suber, on the diversity, composition and network structure of soil fungal and bacterial communities in forests invaded by the exotic pathogen Phytophthora cinnamomi. The belowground footprint of pathogen-driven tree decline implied an increase in the taxonomic and phylogenetic diversity of both bacteria and fungi, but also a severe reduction of tree-symbiotic fungi and Proteobacteria known to have positive effects on plant growth and disease suppression. Moreover, we detected alterations of the topology of soil microbial networks in declining tree neighborhoods (lower connectivity, higher modularity), with implications for ecosystem function. Our findings reveal the large impacts that moderate levels of tree decline can have on the soil microbiome of invaded forests, and highlight the recovery of a functionally diverse and highly connected soil microbiome as a key target in the restoration of these disturbed systems.
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