Generalist taxa shape fungal community structure in cropping ecosystems

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/ edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

IntroductionThrough the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study.MethodsThe soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing.Results and DiscussionThe results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities

Land use conversion to uplands significantly increased the risk of antibiotic resistance genes in estuary area

Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10¯²-1.5 × 10¯¹ copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH4 +), and nitrate (NO3 −), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime

The biogeography of fungal communities in paddy soils is mainly driven by geographic distance

Purpose: The aim of this study is to answer how the biogeographic patterns of fungi are affected by spatial and environmental factors in paddy soils characterized by unique field management. Given the generally low C/N ratios of paddy soils, we also want to test a hypothesis that the dominant fungi in paddy soils are Ascomycota, which reportedly prefer habitats with low soil C/N ratios. Materials and methods: Using quantitative PCR and barcoded pyrosequencing, we investigated the abundance, diversity, and community composition of fungal communities in 30 surface paddy soil samples collected from 10 rice cultivation regions of China. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and variation partition were performed for analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of fungal taxa and their relationships with environmental factors. Results and discussion: The abundance of fungal 18S rRNA gene varied from 106.4 to 108.6 copies g−1 soil, and was positively correlated with soil sand, organic matter, and total nitrogen content, and negatively correlated with soil chloride concentration. Ascomycota comprised 88% of total fungal sequences and increased in relative abundance with increasing soil pH and decreasing mean annual temperature (MAT) and precipitation (MAP). The predominance of Ascomycota in fungal communities is probably due to the low soil C/N ratios (9–15) in the paddy soils studied. The α-diversity increased with MAT, MAP, and soil nitrate-N and total nitrogen content but decreased with soil pH, clay content, chloride concentration, and C/N ratio. Variation partition revealed that fungal β-diversity was mainly driven by geographic distance. Conclusions: In paddy soils which are characterized by intensive rice cropping practices, fungal abundance is mainly influenced by soil properties, fungal α-diversity is constrained by both climatic factors and soil properties, while fungal community compositions are mainly structured by geographic distance. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH4 +), and nitrate (NO3 −), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime

Soil environmental factors rather than denitrification gene abundance control N2O fluxes in a wet sclerophyll forest with different burning frequency

Production of nitrous oxide (N2O) by anaerobic denitrification is one of the most important processes in the global nitrogen (N) cycle and has attracted recent attention due to its significant impacts on climatic change. Fire is a key driver of many ecosystem processes, however, how fire drives the shift in microbial community and thus alters nutrient cycling is still unclear. In this study, a 35-year-old repeated prescribed burning trial, with three treatments (no burning, 2 yearly burning and 4 yearly burning), was used to explore how the long-term repeated prescribed burning affects N2O flux, key soil properties (inorganic N, dissolved organic carbon (DOC) and N, pH, electrical conductivity (EC), moisture), denitrification gene abundance and their interactions. Soil samples were collected in January and April 2011. Quantitative real-time PCR was employed to quantify the gene copy number of target genes, including narG, nirK, nirS and nosZ. In situ N2O fluxes ranged from 0 to 8.8 g N2O–N ha−1 h−1 with an average of 1.47 g N2O–N ha−1 h−1. More frequent fire (2 yearly burning) significantly reduced soil N2O fluxes, availability of C and N substrates and moisture, but increased soil pH and EC compared with no burning and 4 yearly burning treatments. Fire treatments did not significantly affect the abundance of most denitrification genes. There were no significant differences in most parameters measured between the 4 yearly burning and no burning treatments, indicating microbial community function is not affected by less frequent (4 year interval) burning. Variation in the N2O fluxes among the treatments can largely be explained by soil substrate (−3NO, DOC and total soluble nitrogen (TSN)) availability and soil environmental factors (pH, EC, and moisture), while the abundance of most denitrification genes were not related to the N2O fluxes. It is concluded that soil environmental factors rather than denitrification gene abundance control N2O fluxes in this wet sclerophyll forest in response to long-term repeated fires

Effects of nitrogen deposition rates and frequencies on the abundance of soil nitrogen-related functional genes in temperate grassland of northern China

Microbial processes driving nitrogen (N) cycling are hot topics in terms of increasing N deposition. Abundances of N-related functional genes (NFG) can be most responsive to N deposition and commonly used to represent N transformation rates. However, empirically simulated N deposition has been exclusively conducted through large and infrequent N fertilization, which may have caused contrasting effects on NFGs. Therefore, experiments with small and frequent N additions closed to natural deposition are necessary. Independently manipulated N addition rates (i.e., 0, 5, 10, 15, 20, and 50 g N m(-2) year(-1)) and two frequencies (2 times per year addition as conventional large and infrequent N fertilization (2 N), and 12 times per year addition simulating small and frequent N deposition (12 N), respectively) were conducted in a long-term field experiment of a semiarid grassland in northern China. Quantification analysis using real-time PCR were carried out for NFGs, including nifH for N fixation, chiA for N mineralization, archaeal (AOA) and bacterial (AOB) amoA for nitrification, and narG, nirS, nirK, and nosZ for denitrification. NFG abundances showed distinct sensitivities to N addition rates. The nifH, AOA-amoA, nirS, and nosZ gene abundances increased due to improved available N at low N rates, but suppressed by salt toxicity and acidification at high N rates. Large changes of chiA and AOB-amoA gene abundances highlighted their great sensitivities to the N enrichment. The abundance of AOB-amoA was more sensitive to N addition than AOA-amoA, but AOA-amoA dominated in absolute numbers and they predominated the ammonia-oxidation under different conditions. The N addition frequencies caused significant lower gene abundances of nifH, nirS, and nosZ under the 2-N frequency due to stronger suppression of acidification and salt toxicity and resulted in significant higher AOB-amoA gene abundances in response to higher N availability under the 2-N frequency. The NFGs abundances responded to N addition rates distinctly, highlighting that the driven processes involved in N cycling were altered by the N addition rates. The different effects of two N addition frequencies on NFG abundances demonstrated that conventional large and infrequent N fertilization cannot represent N deposition, and small and frequent N addition should be employed to project the effects of N deposition on microbial functional groups as well as on N transformations

The origin of suspended particulate matter in the Great Barrier Reef

Abstract River run-off has long been regarded as the largest source of organic-rich suspended particulate matter (SPM) in the Great Barrier Reef (GBR), contributing to high turbidity, pollutant exposure and increasing vulnerability of coral reef to climate change. However, the terrestrial versus marine origin of the SPM in the GBR is uncertain. Here we provide multiple lines of evidence (13C NMR, isotopic and genetic fingerprints) to unravel that a considerable proportion of the terrestrially-derived SPM is degraded in the riverine and estuarine mixing zones before it is transported further offshore. The fingerprints of SPM in the marine environment were completely different from those of terrestrial origin but more consistent with that formed by marine phytoplankton. This result indicates that the SPM in the GBR may not have terrestrial origin but produced locally in the marine environment, which has significant implications on developing better-targeted management practices for improving water quality in the GBR

Effects of nitrogen deposition rates and frequencies on the abundance of soil nitrogen-related functional genes in temperate grassland of northern China

Microbial processes driving nitrogen (N) cycling are hot topics in terms of increasing N deposition. Abundances of N-related functional genes (NFG) can be most responsive to N deposition and commonly used to represent N transformation rates. However, empirically simulated N deposition has been exclusively conducted through large and infrequent N fertilization, which may have caused contrasting effects on NFGs. Therefore, experiments with small and frequent N additions closed to natural deposition are necessary. Independently manipulated N addition rates (i.e., 0, 5, 10, 15, 20, and 50 g N m(-2) year(-1)) and two frequencies (2 times per year addition as conventional large and infrequent N fertilization (2 N), and 12 times per year addition simulating small and frequent N deposition (12 N), respectively) were conducted in a long-term field experiment of a semiarid grassland in northern China. Quantification analysis using real-time PCR were carried out for NFGs, including nifH for N fixation, chiA for N mineralization, archaeal (AOA) and bacterial (AOB) amoA for nitrification, and narG, nirS, nirK, and nosZ for denitrification. NFG abundances showed distinct sensitivities to N addition rates. The nifH, AOA-amoA, nirS, and nosZ gene abundances increased due to improved available N at low N rates, but suppressed by salt toxicity and acidification at high N rates. Large changes of chiA and AOB-amoA gene abundances highlighted their great sensitivities to the N enrichment. The abundance of AOB-amoA was more sensitive to N addition than AOA-amoA, but AOA-amoA dominated in absolute numbers and they predominated the ammonia-oxidation under different conditions. The N addition frequencies caused significant lower gene abundances of nifH, nirS, and nosZ under the 2-N frequency due to stronger suppression of acidification and salt toxicity and resulted in significant higher AOB-amoA gene abundances in response to higher N availability under the 2-N frequency. The NFGs abundances responded to N addition rates distinctly, highlighting that the driven processes involved in N cycling were altered by the N addition rates. The different effects of two N addition frequencies on NFG abundances demonstrated that conventional large and infrequent N fertilization cannot represent N deposition, and small and frequent N addition should be employed to project the effects of N deposition on microbial functional groups as well as on N transformations