查看更多>>摘要：Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great po-tential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how as-sumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial commu-nities. However, this approach is unfortunately often used to draw conclusions which are far beyond the sci-entific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.
Du Preez, GerhardDaneel, MiekeDe Goede, RonDu Toit, Marie Joey...
14页
查看更多>>摘要：The health and functioning of soil ecosystems are the foundation of sustainable food production and land management. Of key importance in achieving sustainability, is the frequent measurement of soil health, and indices based on the community structure of nematodes are amongst the most widely used toolsets by soil ecologists. Thirty years after the development of the Maturity Index, we aimed to evaluate the application, utility, and future directions of nematode-based indices (NBIs). This review focused on NBIs that are calculated using the coloniser-persister classification of nematodes. Data from 672 empirical studies in terrestrial environments revealed that the NBIs presented a dissimilar usage trend. The Channel Index and Metabolic Footprints showed the strongest increase in application rates over time, thus indicating a greater interest in studying decomposition pathways and ecosystem functioning, respectively. Furthermore, nematode-based indices were mostly applied in agricultural systems associated with herbaceous crops and in studies investigating, for example, soil nutrient enrichment following manure and/or inorganic fertilizer application. We further provide a framework for selecting a focus-orientated subset of NBIs for testing hypotheses based on the underlying ecological mechanisms. Also, we highlight important considerations, including the unexpected behaviour of some nematode taxa, in the interpretation of NBIs. The improvement of NBIs relies on advancing our understanding of the autecology of nematodes. Finally, we deliver insight into the further development of NBIs considering recent methodological advancements. We highlight that NBIs have been and might become increasingly important in providing valuable information on soil ecosystem health and functioning, especially considering the urgent need for more sustainable land use.
查看更多>>摘要：Organic amendments stimulate carbon (C) mineralization by affecting the soil nutrient content, soil organic carbon (SOC) chemistry, and microbial community structure, especially keystone taxa. Exogenous substrates' quality is expected to affect the relative importance of these biotic and abiotic factors in C mineralization. However, little evidence from long-term studies has been found, and the underlying mechanisms remain unclear. Therefore, this study investigated how exogenous substrate quality affects the changes in keystone taxa and their relative contribution to C mineralization in comparison with soil nutrient content and SOC chemistry in a longterm field experiment. Six fertilization treatments from a 30-year field experiment were selected. To investigate the impact of substrate quality, the six treatments were sorted into three groups: non-organic-amended group, including no fertilization and inorganic N fertilizer; green manure-amended groups, including full amount of green manure input and 50% green manure plus 50% inorganic N fertilizer; and wheat straw-amended group, including full amount of wheat straw input and 50% wheat straw plus 50% inorganic N fertilizer. Our results confirmed that the relative importance of keystone taxa on C mineralization varied according to the exogenous substrates' quality. In the non-organic-amended group, the keystone taxa belonged to Betaproteobacteriales, and the keystone Betaproteobacteriales module, from guided network analysis, was associated with higher C mineralization. In the wheat straw-amended treatments, the keystone taxa Chaetomiaceae module had a dominant influence on C mineralization. In contrast, in the green manure-amended treatments, the keystone taxa in Subgroups 4 and 6 of Acidobacteria and Alphaproteobacteria had a limited impact on the C mineralization rate, whereas the increased aromatic C component was an important explanatory variable associated with C mineralization. In conclusion, this study confirmed that exogenous organic substrate quality affects the occurrence of keystone microbial taxa linked to soil C mineralization.
查看更多>>摘要：Energy flux in food webs, i.e., energy consumption by different trophic groups and describing their energetic structure, has been proposed as a powerful tool to understand the relationships between biodiversity and multiple ecosystem functions (ecosystem multifunctionality). Here we examined how different fertilization regimes affected the energy flux across multitrophic levels of soil nematodes in the paddy rice and upland maize fields. We considered 13 ecosystem functions of four ecological processes related to plant productivity, nutrient cycling processes and drivers, and functional stability, which are central to energy and nutrient flow across trophic levels. To confirm whether multitrophic flux would underpin the relationships between biodiversity and multifunctionality, we compared energy flux with other approaches including taxonomic diversity, functional diversity and community composition. Results showed that organic fertilizer supported 33-340% greater multitrophic energy flux of soil nematode community and enhanced 41-264% of ecosystem multifunctionality in both fields compared with mineral fertilizer treatments. Organic fertilization enhanced ecosystem multi functionality by favoring energy flux in multitrophic levels of soil nematodes, while fertilization-mediated changes in other facets of biodiversity were less related to multifunctionality. Our study provides empirical evidence that energy flux within food webs can be used to understand the impacts of environmental change drivers on ecosystem multifunctionality.
查看更多>>摘要：Anthropogenic activities have severely altered biogeochemical cycles with far-reaching consequences for biodiversity and ecosystem functioning. The use of artificial fertilizers, increased legume cultivation and fossil fuel combustion has resulted in a twofold increase of inorganic nitrogen input in natural ecosystems worldwide, often with considerable negative effects on plant and microbial communities. However, not all ecosystems are as sensitive to increased nitrogen deposition and effects may vary among ecological and taxonomic groups. Here, we studied how increasing nitrogen deposition affected soil and root-associated microbial communities of plants growing in ombrotrophic bogs. We specifically tested the hypothesis that microbiomes of plants with different mycorrhizal types respond differently to increased nitrogen deposition. We sampled soil and the roots of three plant species of different mycorrhizal types - arbuscular mycorrhizal (Molinia caerulea), ectomycorrhizal (Betula pubescens), ericoid mycorrhizal (Vaccinium oxycoccos) - and a non-mycorrhizal plant species (Eriophorum vagi-natum) along a nitrogen deposition gradient in Europe (5-30 kg N ha(-1) year(-1)). For each sample, the fungal and bacterial biomass and community composition were assessed and related to current levels of nitrogen deposition. In general, we found that fungi were more strongly affected by increased nitrogen deposition than bacteria. Fungal biomass, richness and diversity significantly decreased with increasing nitrogen deposition while bacterial biomass, richness and diversity was indifferent. OTU richness, diversity or community composition of ericoid mycorrhizal fungi did not change with increasing nitrogen deposition, while ectomycorrhizal fungal OTU richness and diversity significantly declined and community composition changed. We did not find an increase in arbuscular mycorrhizal fungi biomass along this gradient, despite the strong increase in abundance of the arbuscular mycorrhizal plant M. caerulea with increasing nitrogen deposition. We conclude that atmospheric nitrogen deposition has stronger effects on fungal than on bacterial communities in ombrotrophic bogs and that fungal guilds differ in their response.
查看更多>>摘要：Iron (oxyhydr)oxides [Fe(III)] are important adsorbents of arsenate [As(V)] and phosphate in paddy soils, and microbial Fe(III) reduction is hence central to biogeochemical cycles of arsenic and phosphorus. Nevertheless, how Fe(III) reducers and As(V) reducers at the community level respond to As(V) and phosphate adsorption in paddy soils remain unclear. Here, we explored the influences of arsenate and/or phosphate adsorption to fer-rihydrite on active acetate-dependent Fe(III)-reducing and As(V)-reducing microbial communities in a paddy soil, using C-13-acetate-based rRNA-stable isotope probing (SIP). During anaerobic SIP incubations, the arsenate and/or phosphate adsorption to ferrihydrite retarded Fe(III) reduction to various extents, with arsenate alone or combined with phosphate having greater inhibitory effects than phosphate alone. 16S rRNA-based sequencing results revealed that the adsorption of arsenate alone or combined with phosphate markedly enriched several Fe (III) reducers that have also been found to enable arsenate reduction, especially Geobacter genus. This was coincided with the pronounced increment in transcript abundance of arsenate-respiring gene (arrA) induced by the presence of arsenate and further confirmed by cloning and sequencing result which indicated that Geobacter spp. harboring arrA gene were the major As(V) reducers herein. In contrast, the presence of arsenate led to a remarkable decline in other Fe(III) reducers, including Dechloromonas and Thermincola genera, which have rarely been reported to be related to arsenate transformation. Furthermore, all these identified Fe(III) reducers declined significantly by phosphate adsorption alone. Additionally, the adsorption of phosphate to ferrihydrite not only boosted the reduction of adsorbed As(V), but also enriched the respiratory As(V)-reducing microbes containing arrA gene. These findings demonstrate that the adsorption of arsenate and/or phosphate inhibits Fe(III) reduction while promotes As(V) reduction, and shifts the Fe(III)-reducing and As(V)-reducing microbial communities in paddy soils. Overall this study provides novel insights into intricate biogeochemical coupling between iron, arsenic and phosphorus in paddy soils.
查看更多>>摘要：Mollisols have a high potential to mitigate climate change and play an important role in the global carbon (C) cycle due to their inherently high soil organic matter (SOM). However, little is known about the mechanism of C stabilization in Mollisols, especially subjected to different management effects. To trace C stabilization between aggregates and SOM density fractions in Mollisols, soil samples were collected from different experimental plots: controlled irrigation + rice (Oryza sativa L.) straw removal (CI), flooded irrigation + rice straw removal (FI), controlled irrigation + rice straw return (CI-SR), and flooded irrigation + rice straw return (FI-SR). Each soil sample was separated into three aggregate size classes (> 250 pm, 53-250 pm, and < 53 pm), then each class individually subjected to density fractionation to obtain free and occluded light fractions (fLF and oLF), as well as dense and mineral-heavy fractions (DF and MF). The overall C content and 13C abundance of fractions were measured to interpret C transfer and accumulation among aggregate and density fractions. The highest increase in the soil organic C (9.27-24.88%) was observed in CI-SR compared with the other treatments. Irrigation and straw return primarily affected C accumulation within macroaggregates and the MF, which were the dominant forms in the aggregates and density fractions, respectively. An enrichment in delta C-13 was found from macroaggregates to silt + clay, and from light to heavy fractions, indicating that Mollisols macroaggregates and light fractions acted as the source or initial store of plant residues, and that the C in the silt + clay class and heaviest fraction contained more microbially-transformed C than did the macroaggregates and light fractions. A detailed scheme of C transfer within aggregates and SOM fractions based on the delta C-13 natural abundance revealed the following general sequence: free light -> occluded light -> dense -> mineral fractions, concurring with results reported at upland sites. There is a greater probability of C transfer between SOM density fractions under CI. This contrasted with the results that CI decreases the possibility of C exchange between aggregates than FI, which indicates differences in the C stabilization processes between no-flooded and flooded conditions of Mollisols. In addition, straw returning can reduce the possibility of C exchange both between and within aggregates, which plays a significant role in maintaining the stability of the Mollisols carbon cycle. The present study provides further detailed insights into the C stabilizing mechanisms in Mollisols which depend on management (straw, water status). This finding is conducive to the sustainable use and management of Mollisols toward maintaining or increasing C stock and in realizing the objective of C-neutral agriculture.
Chiewattanakul, MashitaMcAleer, Adam D. A.Reay, Michaela K.Griffiths, Robert, I...
10页
查看更多>>摘要：Biological nitrogen fixation (BNF) performed by diazotrophs is vital to our understanding of ecosystem functions, as plant nitrogen (N) is commonly a limiting nutrient for primary productivity. However, significant limitations have remained in our knowledge of the controls and rates of this process, due to technical difficulties in directly quantifying nitrogen (N-2) fixation rates. To address this, we developed a novel compound-specific N-15-stable isotope probing method involving analysis of acid hydrolysable soil amino acids (AAs) by gas chromatography combustion-isotope ratio mass spectrometry (GC-C-IRMS) for the quantification of BNF in soils. By analysing N-15 enriched AAs (as N-acetyl, O-isopropyl derivatives), this new approach aimed to provide greater specificity compared to existing methods, and to contribute previously unobtainable quantitative information on the capture and flow of N-2 fixed in soils. Laboratory incubations using N-15(2) gas were carried out on surface peat over 15 days to obtain quantitative measures of N-2 fixation by the microbial community. Longer incubations with the addition of a glucose energy source significantly increased the level of N-15 enrichment, i.e. N fixed. The enhanced detection limits of N-15-AAs by GC-C-IRMS, compared to bulk soil delta N-15 value determinations, was key to assessments of N-2 fixation. Valuable insights into the assimilation pathway of the applied N-15(2)-substrate were revealed; for peat soils, N-15 incorporation into glutamate dominated over other AAs.
查看更多>>摘要：The carbon sequestration potential of biochar depends on its stability in the soil and its priming effect on native soil organic carbon mineralization, which could be expected to be in turn affected by biochar processing, aging and soil clay content. This study applied stable carbon isotopes (delta C-13) to quantify the mineralization of fresh and aged biochar pyrolyzed at 300, 450, and 600 degrees C and their priming effects on native soil organic carbon in two types of soils with different clay contents. At the end of the incubation, the total carbon loss of biochar-amended soil was 16-53% lower than that of unamended soil and the lowest carbon loss was found in soils amended with 600 degrees C biochar. Regardless of soil type, the proportion of biochar-carbon (carbon in the biochar) mineralized decreased with increasing pyrolysis temperature. For fresh biochar, the proportion of carbon mineralized was 13-47% higher in the sandy loam soil than in the sandy clay loam soil at the end of the incubation. However, soil type had a minimal effect on the mineralization proportion of aged biochar-carbon. The dissolved organic carbon increased after fresh and aged biochar was added to the sandy clay loam, but not the sandy loam, suggesting less carbon hydrolysis and solubilization from native soil organic carbon and biochar in the sandy loam soil. Moreover, biochar amendment increased the enzyme activities in sandy clay loam soil and either increased or had no effect on those in sandy loam soil. Fresh biochar had no effect on native soil organic carbon mineralization after it was applied, although a negative priming effect was observed after two-7 wk. For aged biochar, a negative priming effect was found for both soils. These findings demonstrated that biochar was more stable in clayey soils, and biochar produced at higher temperature indeed showed high soil carbon sequestration potential.
查看更多>>摘要：Biological soil crusts (biocrusts), specialized communities of cyanobacteria, lichens, mosses, fungi and bacteria occurring on the ground surface, are key drivers of soil carbon (C) cycles in drylands, yet our understanding of how biocrusts directly and indirectly (through soil temperature or moisture) affect soil respiration and the contributions of biocrusts to soil C efflux is very limited. Using continuous field measurements in bare and biocrusted soils, we assessed the influence of biocrusts on soil respiration and the biocrust contribution to soil respiration over a one-year period and explained the mechanisms by which biocrusts directly and indirectly regulate soil respiration. Although the overall effect of biocrusts on soil respiration was positive, contrasting effects of biocrusts on soil respiration were also found. Unfortunately, the indirect effect of biocrusts on soil respiration through soil temperature or moisture was nonsignificant. The driving factor of total soil respiration was soil temperature, but soil moisture, photosynthetically active radiation and precipitation were driving factors for soil respiration in the biocrust layer. We proposed conceptual frameworks to explain the contrasting mechanisms by which biocrusts modulate soil respiration. In addition, biocrusts decreased the temperature sensitivity of soil respiration. Our findings indicate that biocrusts may alter the driving factors, forming contrasting mechanisms to regulate soil respiration in the biocrust layer, and emphasize the important roles of biocrusts as modulators of C cycles in dryland soils. Incorporating biocrusts into terrestrial C process models may improve predictions of climate change impacts on dryland ecosystems.
NSTL
Elsevier