Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River.

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny.

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

Vegetation restoration effects on soil carbon and nutrient concentrations and enzymatic activities in post-mining lands are mediated by mine type, climate, and former soil properties.

Vegetation restoration is a widely used, effective, and sustainable method to improve soil quality in post-mining lands. Here we aimed to assess global patterns and driving factors of potential vegetation restoration effects on soil carbon, nutrients, and enzymatic activities. We synthesized 4838 paired observations extracted from 175 publications to evaluate the effects that vegetation restoration might have on the concentrations of soil carbon, nitrogen, and phosphorus, as well as enzymatic activities. We found that (1) vegetation restoration had consistent positive effects on the concentrations of soil organic carbon, total nitrogen, available nitrogen, ammonia, nitrate, total phosphorus, and available phosphorus on average by 85.4, 70.3, 75.7, 54.6, 58.6, 34.7, and 60.4 %, respectively. Restoration also increased the activities of catalase, alkaline phosphatase, sucrase, and urease by 63.3, 104.8, 125.5, and 124.6 %, respectively; (2) restoration effects did not vary among different vegetation types (i.e., grass, tree, shrub and their combinations) or leaf type (broadleaved, coniferous, and mixed), but were affected by mine type; and (3) latitude, climate, vegetation species richness, restoration year, and initial soil properties are important moderator variables, but their effects varied among different soil variables. Our global scale study shows how vegetation restoration can improve soil quality in post-mining lands by increasing soil carbon, nutrients, and enzymatic activities. This information is crucial to better understand the role of vegetation cover in promoting the ecological restoration of degraded mining lands.

Effects of drying-rewetting cycles on the fluxes of soil greenhouse gases.

Irregular precipitation caused by climate changes has resulted in frequent events of soil drying-rewetting cycles (DWC), which can strongly affect soil carbon (C) and nitrogen (N) cycling, including the fluxes of greenhouse gases (GHGs). The response of soil carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes to DWC events may differ among different ecosystem types and vary with experimental settings and soil properties, but these processes were not quantitatively assessed. Here, we evaluated the responses of soil GHG fluxes to DWC, compared with consistent moisture, as well as the associated driving factors with 424 paired observations collected from 47 publications of lab incubation experiments. Results showed that: (1) DWC significantly decreased soil CO2 emissions by an average of 9.7%, but did not affect the emissions and uptakes of soil CH4 and N2O; (2) DWC effects on soil GHG emissions varied significantly among different ecosystem types, with CO2 emissions significantly decreased by 6.8 and 16.3% in croplands and grasslands soils, respectively, and CH4 and N2O emissions significantly decreased and increased in wetlands and forests soils, respectively; (3) the effects of DWC on CO2 emissions were also positively regulated by organic C and N concentrations, pH, clay concentration, and soil depth, but negatively by C:N ratio and silt concentration, while DWC effects on N2O emissions were negatively controlled by C:N ratio, silt concentration, and soil depth. Overall, our results showed that CO2 emissions were significantly decreased by DWC, while the fluxes of CH4 and N2O were not affected, indicating an overall decrease of GHGs in response to DWC. Our results will be useful for a better understanding of global GHG emissions under future climate change scenario.

Global patterns and driving factors of plant litter iron, manganese, zinc, and copper concentrations.

Plant litter decomposition is not only the major source of soil carbon and macronutrients, but also an important process for the biogeochemical cycling of trace elements such as iron (Fe), manganese (Mn), zinc (Zn), and copper (Cu). The concentrations of plant litter trace elements can influence litter decomposition and element cycling across the plant and soil systems. Yet, a global perspective of the patterns and driving factors of trace elements in plant litter is missing. To bridge this knowledge gap, we quantitatively assessed the concentrations of four common trace elements, namely Fe, Mn, Zn, and Cu, of freshly fallen plant litter with 1411 observations extracted from 175 publications across the globe. Results showed that (1) the median of the average concentrations of litter Fe, Mn, Zn, and Cu were 0.200, 0.555, 0.032, and 0.006 g/kg, respectively, across litter types; (2) litter concentrations of Fe, Zn, and Cu were generally stable regardless of variations in multiple biotic and abiotic factors (e.g., plant taxonomy, climate, and soil properties); and (3) litter Mn concentration was more sensitive to environmental conditions and influenced by multiple factors, but mycorrhizal association and soil pH and nitrogen concentration were the most important ones. Overall, our study provides a clear global picture of plant litter Fe, Mn, Zn, and Cu concentrations and their driving factors, which is important for improving our understanding on their biogeochemical cycling along with litter decomposition processes.

Eimeria infections of plateau pika altered the patterns of temporal alterations in gut bacterial communities.

Intestinal parasites, such as Eimeria, are common among plateau pika (Ochotona curzoniae). The gut microbiome is an essential driver of the host response to gastrointestinal parasites. However, the effects of intestinal protozoal parasites on the temporal variations in the gut microbiome and behavioral and physiological activities remain unknown. Our study conducted treatments involving experimental feeding of pika with Eimeria oocysts or anticoccidia under laboratory conditions to focus on the parasite-associated alterations in gut bacterial communities, host behavioral activity, physiology, and host-bacteria relationships. The results showed insignificant differences in bacterial community structures among treatments on the basis of Bray-Curtis distance metrics, whereas the patterns of temporal alterations in the bacterial communities were changed by the treatments. Bacterial alpha diversities did not vary with the treatments, and experimental feeding with Eimeria slowed down the decrement rate of alpha diversity. Furthermore, few bacterial members were significantly changed by the treatments-only the genus Ruminococcus and the species Ruminococcus flavefaciens, which were associated with energy metabolism. Experimental feeding with Eimeria modified the temporal variations in the bacterial members, including a lower loss rate of the relative abundance of the dominant families Muribaculaceae and Ruminococcaceae in the group with Eimeria experimental feeding. Moreover, a shifting energy trade-off was suggested by the parasite-induced increments in thyroid hormones (triiodothyronine and tetraiodothyronine) and decrements in exploration behavior in the group with Eimeria feeding. However, we did not detect specific connections between gut bacterial communities and pika behaviors and physiology in terms of energy trade-offs. Further in-depth research is needed to examine the role of Eimeria-modified differences in the gut bacteria of plateau pika.

Global distribution of soil fauna functional groups and their estimated litter consumption across biomes.

Soil invertebrates (i.e., soil fauna) are important drivers of many key processes in soils including soil aggregate formation, water retention, and soil organic matter transformation. Many soil fauna groups directly or indirectly participate in litter consumption. However, the quantity of litter consumed by major faunal groups across biomes remains unknown. To estimate this quantity, we reviewed > 1000 observations from 70 studies that determined the biomass of soil fauna across various biomes and 200 observations from 44 studies on litter consumption by soil fauna. To compare litter consumption with annual litterfall, we analyzed 692 observations from 24 litterfall studies and 183 observations from 28 litter stock studies. The biomass of faunal groups was highest in temperate grasslands and then decreased in the following order: boreal forest > temperate forest > tropical grassland > tundra > tropical forest > Mediterranean ecosystems > desert and semidesert. Tropical grasslands, desert biomes, and Mediterranean ecosystems were dominated by termites. Temperate grasslands were dominated by omnivores, while temperate forests were dominated by earthworms. On average, estimated litter consumption (relative to total litter input) ranged from a low of 14.9% in deserts to a high of 100.4% in temperate grassland. Litter consumption by soil fauna was greater in grasslands than in forests. This is the first study to estimate the effect of different soil fauna groups on litter consumption and related processes at global scale.

Mycorrhizal association and life form dominantly control plant litter lignocellulose concentration at the global scale.

Lignocellulose is a major component of plant litter and plays a dominant role in regulating the process of litter decomposition, but we lack a global perspective on plant litter initial lignocellulose concentration. Here, we quantitatively assessed the global patterns and drivers of litter initial concentrations of lignin, cellulose, and hemicellulose using a dataset consisting of 6,021 observations collected from 795 independent publications. We found that (1) globally, the median concentrations of leaf litter lignin, cellulose, and hemicellulose were 20.3, 22.4, and 15.0% of litter mass, respectively; and (2) litter initial concentrations of lignin, cellulose, and hemicellulose were regulated by phylogeny, plant functional type, climate, and soil properties, with mycorrhizal association and lifeform the dominant predictors. These results clearly highlighted the importance of mycorrhizal association and lifeform in controlling litter initial lignocellulose concentration at the global scale, which will help us to better understand and predict the role of lignocellulose in global litter decomposition models.

Contrasting effects of altered precipitation regimes on soil nitrogen cycling at the global scale.

Changes in precipitation regimes can strongly affect soil nitrogen (N) cycling in terrestrial ecosystems. However, whether altered precipitation regimes may differentially affect soil N cycling between arid and humid biomes at the global scale is unclear. We conducted a meta-analysis using 1036 pairwise observations collected from 194 publications to assess the effects of increased and decreased precipitation on the input (N return from plants), storage (various forms of N in soil), and output (gaseous N emissions) of soil N in arid versus humid biomes at the global scale. We found that (1) increased precipitation significantly increased N input (+12.1%) and output (+34.9%) but decreased N storage (-13.7%), while decreased precipitation significantly decreased N input (-10.7%) and output (-34.8%) but increased N storage (+11.1%); (2) the sensitivity of soil N cycling to increased precipitation was higher in arid regions than in humid regions, while that to decreased precipitation was lower in arid regions than in humid regions; (3) the effect of altered precipitation regimes on soil N cycling was independent of precipitation type (i.e., rainfall vs. snowfall); and (4) the mean annual precipitation regulated soil N cycling in precipitation alteration experiments at the global scale. Overall, our results clearly show that the response of soil N cycling to increased versus decreased precipitation differs between arid and humid regions, indicating the uneven effect of climate change on soil N cycling between these two contrasting climate regions. This implies that ecosystem models need to consider the differential responses of N cycling to altered precipitation regimes in different climatic conditions under future global change scenarios.

Litter quality and stream physicochemical properties drive global invertebrate effects on instream litter decomposition.

Plant litter is the major source of energy and nutrients in stream ecosystems and its decomposition is vital for ecosystem nutrient cycling and functioning. Invertebrates are key contributors to instream litter decomposition, yet quantification of their effects and drivers at the global scale remains lacking. Here, we systematically synthesized data comprising 2707 observations from 141 studies of stream litter decomposition to assess the contribution and drivers of invertebrates to the decomposition process across the globe. We found that (1) the presence of invertebrates enhanced instream litter decomposition globally by an average of 74%; (2) initial litter quality and stream water physicochemical properties were equal drivers of invertebrate effects on litter decomposition, while invertebrate effects on litter decomposition were not affected by climatic region, mesh size of coarse-mesh bags or mycorrhizal association of plants providing leaf litter; and (3) the contribution of invertebrates to litter decomposition was greatest during the early stages of litter mass loss (0-20%). Our results, besides quantitatively synthesizing the global pattern of invertebrate contribution to instream litter decomposition, highlight the most significant effects of invertebrates on litter decomposition at early rather than middle or late decomposition stages, providing support for the inclusion of invertebrates in global dynamic models of litter decomposition in streams to explore mechanisms and impacts of terrestrial, aquatic, and atmospheric carbon fluxes.

Responses of soil fauna communities to the individual and combined effects of multiple global change factors.

Soil fauna plays a key role in regulating biogeochemical cycles, but how multiple global change factors (GCFs) may affect faunal communities remains poorly studied. We conducted a meta-analysis using 1154 observations to evaluate the individual and combined effects of elevated CO2 , nitrogen (N) addition, warming, increased rainfall and drought on soil fauna density and diversity. Here we show that, overall, individual and combined effects of GCFs had negligible effects on soil fauna density and diversity, except that density was negatively affected by drought (-27.4%) and positively affected by increased rainfall individually (+24.9%) and in combination with N addition (+67.3%) or warming (+70.4%). GCF effects varied among taxonomic groups both in magnitude and direction. Variables such as latitude, elevation and experimental setting significantly impacted both individual and combined effects. Our results suggest that soil fauna density is affected by changed rainfall regimes, while diversity is resistant against individual and combined effects of multiple GCFs.

Global patterns and drivers of initial plant litter ash concentration.

Ash is a fundamental component of plant litter and plays a vital role in regulating litter decomposition. However, to date, global patterns and underlying mechanisms of initial litter ash concentrations remain unclear. Here, we used 570 observations collected from 104 independent publications to assess the global patterns of initial plant litter ash concentrations and evaluated the effects of mycorrhizal association [arbuscular mycorrhiza (AM) vs. ectomycorrhiza (ECM)], taxon group (gymnosperm vs. angiosperm), life form (tree vs. shrub vs. herb), leaf type (broadleaf vs. needle), and environmental factors such as climate and soil properties on initial litter ash concentration. The results showed that (1) global average ash concentrations varied significantly among different plant tissues and were 7.3, 4.5, 3.7, 3.5, 3.1, 2.4, and 1.5% in leaf, root, bark, reproductive tissue (flower and fruit), branch, stem, and wood litter, respectively; (2) in leaf litter, the initial ash concentrations of AM plants and species associated with both AM and ECM fungi were higher than those of ECM plants, and those of the tree species were lower than those of the herbs and shrubs; in root litter, the initial ash concentrations of the AM plants were lower than those of the species associated with both AM and ECM fungi but higher than those of the ECM plants; in both leaf and root litter, the initial ash concentrations of the angiosperms and broadleaf trees were higher than those of the gymnosperms and needle trees, respectively, while the effect of plant traits on branch litter was not obvious; and (3) the initial ash concentration of leaf litter was predominantly driven by mycorrhizal association and taxon group, while that of root litter tended to be driven by mycorrhizal association well as soil organic carbon. Our study clearly assessed the global patterns and underlying mechanisms of initial plant litter ash concentrations, which could help in better understanding the role of ash in litter decomposition and the related processes of carbon and nutrient cycling.

Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities.

The mechanisms underlying microbial community dynamics and co-occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co-occurrence complexity and in the average pairwise phylogenetic distances between co-occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic relatedness between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.

Dynamics of Soil Bacterial and Fungal Communities During the Secondary Succession Following Swidden Agriculture IN Lowland Forests.

Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.

Soil microbial interconnections along ecological restoration gradients of lowland forests after slash-and-burn agriculture.

Microbial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities in response to slash-and-burn practice and a spontaneous restoration (spanning ca. 60 years) of tropical forests after the practice, in Papua New Guinea. We found significantly higher complexity and greater variations in fungal networks than in those of bacteria, despite no significant changes observed in bacterial or fungal networks across successional stages. Within most successional stages, bacterial core co-occurrences (co-occurrences consistently present across all sub-networks in a stage) were more frequent than those of fungi, indicating higher stability of interconnections between bacteria along succession. The stable interconnections occurred frequently between bacterial taxa (i.e. Sporosarcina, Acidimicrobiale and Bacillaceae) and between ectomycorrhizal fungi (Boletaceae and Russula ochroleuca), implying important ecological roles of these taxa in the ecosystem restoration. Collectively, our results provide new insight into microbial interconnections in response to slash-and-burn agriculture and the subsequent ecosystem restoration, thus promoting a better understanding of microbial roles in ecosystem services and restoration.

Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process.

Temperature plays crucial roles in microbial interactions that affect the stability and performance of anaerobic digestion. In this study, the microbial interactions and their succession in the anaerobic digestion process were investigated at three levels, represented by (1) present and (2) active micro-organisms, and (3) gene expressions under a temperature gradient from 25 to 55 °C. Network topological features indicated a global variation in microbial interactions at different temperatures. The variations of microbial interactions in terms of network modularity and deterministic processes based on topological features, corresponded well with the variations of methane productions, but not with temperatures. A common successional pattern of microbial interactions was observed at different temperatures, which showed that both deterministic processes and network modularity increased over time during the digestion process. It was concluded that the increase in temperature-mediated network modularity and deterministic processes on shaping the microbial interactions improved the stability and efficiency of anaerobic digestion process.

Diet Diversity Is Associated with Beta but not Alpha Diversity of Pika Gut Microbiota.

Wild mammals often consume different food sources as they become geographical available. This change in diet composition is likely to influence the gut microbial community, yet it remains unclear what the relationship looks like-particularly in small herbivores-under natural conditions. We used DNA sequencing approaches to characterize the diet composition and gut microbial community of wild plateau pikas (Ochotona curzoniae) collected from three altitudes. We tested if diet and gut microbiota composition changes across altitudes, and the relationship between diet diversity and gut microbiota diversity. Our results showed that altitude significantly influences the composition of diet and gut microbial communities. Notably, the alpha diversity (Shannon diversity and observed OTUs) of individual diet was not significantly correlated with that of gut microbiota, whereas the beta diversity (Jaccard and Bray-Curtis dissimilarity) of diet was positively correlated with that of gut microbiota. Our study is the first time to highlight the relationship between diet and gut microbiota composition in wild pikas on the Qinghai-Tibet Plateau. It suggests that the species richness within individual gut microbiota does not linearly increase with diet diversity, whereas those individuals that are more similar in diet composition harbor more similar gut microbiota.