A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth.

Introduction: Endophytic microorganisms are bacteria or fungi that inhabit plant internal tissues contributing to various biological processes of plants. Some endophytic microbes can promote plant growth, which are known as plant growth-promoting endophytes (PGPEs). There has been an increasing interest in isolation and identification of PGPEs for sustainable production of crops. This study was undertaken to isolate PGPEs from roots of a halophytic species Sesuvium portulacastrum L. and elucidate potential mechanisms underlying the plant growth promoting effect. Methods: Surface-disinfected seeds of S. portulacastrum were germinated on an in vitro culture medium, and roots of some germinated seedlings were contaminated by bacteria and fungi. From the contamination, an endophytic fungus called BF-F (a fungal strain isolated from bacterial and fungal contamination) was isolated and identified. The genome of BF-F strain was sequenced, its genome structure and function were analyzed using various bioinformatics software. Additionally, the effect of BF-F on plant growth promotion were investigated by gene cluster analyses. Results: Based on the sequence homology (99%) and phylogenetic analysis, BF-F is likely a new Cladosporium angulosum strain or possibly a new Cladosporium species that is most homologous to C. angulosum. The BF-F significantly promoted the growth of dicot S. portulacastrum and Arabidopsis as well as monocot rice. Whole genome analysis revealed that the BF-F genome has 29,444,740 bp in size with 6,426 annotated genes, including gene clusters associated with the tryptophan synthesis and metabolism pathway, sterol synthesis pathway, and nitrogen metabolism pathway. BF-F produced indole-3-acetic acid (IAA) and also induced the expression of plant N uptake related genes. Discussion: Our results suggest that BF-F is a novel strain of Cladosporium and has potential to be a microbial fertilizer for sustainable production of crop plants. The resulting genomic information will facilitate further investigation of its genetic evolution and its function, particularly mechanisms underlying plant growth promotion.

Proteomic and metabolomic analyses uncover integrative mechanisms in Sesuvium portulacastrum tolerance to salt stress.

Introduction: Salt stress is a major constraint affecting crop productivity worldwide. Investigation of halophytes could provide valuable information for improving economically important crops to tolerate salt stress and for more effectively using halophytes to remediate saline environments. Sesuvium portulacastrum L. is a halophyte species widely distributed in tropical and subtropical coastal regions and can absorb a large amount of sodium (Na). This study was to analyze S. portulacastrum responses to salt stress at morphological, physiological, proteomic, and metabolomic levels and pursue a better understanding of mechanisms behind its salt tolerance. Methods: The initial experiment evaluated morphological responses of S. portulacastrum to different concentrations of NaCl in a hydroponic system, and subsequent experiments compared physiological, proteomic, and metabolomic changes in S. portulacastrum after being exposed to 0.4 M NaCl for 24 h as immediate salt stress (IS) to 14 days as adaptive salt stress (AS). Through these analyses, a working model to illustrate the integrative responses of S. portulacastrum to salt stress was proposed. Results: Plants grown in 0.4 M NaCl were morphologically comparable to those grown in the control treatment. Physiological changes varied in control, IS, and AS plants based on the measured parameters. Proteomic analysis identified a total of 47 and 248 differentially expressed proteins (DEPs) in leaves and roots, respectively. KEGG analysis showed that DEPs, especially those occurring in roots, were largely related to metabolic pathways. Root metabolomic analysis showed that 292 differentially expressed metabolites (DEMs) occurred in IS plants and 371 in AS plants. Among them, 20.63% of upregulated DEMs were related to phenolic acid metabolism. Discussion: Based on the integrative analysis of proteomics and metabolomics, signal transduction and phenolic acid metabolism appeared to be crucial for S. portulacastrum to tolerate salt stress. Specifically, Ca2+, ABA, and JA signalings coordinately regulated salt tolerance in S. portulacastrum. The stress initially activated phenylpropanoid biosynthesis pathway through Ca2+ signal transduction and increased the content of metabolites, such as coniferin. Meanwhile, the stress inhibited MAPK signaling pathway through ABA and JA signal transduction, which promoted Na sequestration into the vacuole to maintain ROS homeostasis and enhanced S. portulacastrum tolerance to salt stress.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China.

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Microorganisms carrying nosZ I and nosZ II share similar ecological niches in a subtropical coastal wetland.

Nitrous oxide (N2O) reducers are the only known sink for N2O and pivotal contributors to N2O mitigation in terrestrial and water ecosystems. However, the niche preference of nosZ I and nosZ II carrying microorganisms, two divergent clades of N2O reducers in coastal wetlands, is not yet well documented. In this study, we investigated the abundance, community structure and co-occurrence network of nosZ I and nosZ II carrying microorganisms and their driving factors at three depths in a subtropical coastal wetland with five plant species and a bare tidal flat. The taxonomic identities differed between nosZ I and nosZ II carrying microorganisms, with nosZ I sequences affiliated with Alphaproteobacteria and Betaproteobacteria while nosZ II sequences with Gemmatimonadetes, Verrucomicrobia, Gammaproteobacteria, and Chloroflexi. The abundances of nosZ I and nosZ II decreased with increasing soil depths, and were positively associated with salinity, total carbon (TC) and total nitrogen (TN). Random forest analysis showed that salinity was the strongest predictor for the abundances of nosZ I and nosZ II. Salinity, TC and TN were the major driving forces for the community structure of nosZ I and nosZ II carrying microorganisms. Moreover, co-occurrence analysis showed that 92.2 % of the links between nosZ I and nosZ II were positive, indicating that nosZ I and nosZ II carrying microorganisms likely shared similar ecological niches. Taken together, we provided new evidence that nosZ I and nosZ II carrying microorganisms shared similar ecological niches in a subtropical estuarine wetland, and identified salinity, TC and TN serving as the most important environmental driving forces. This study advances our understanding of the environmental adaptation and niche preference of nosZ I and nosZ II carrying microorganisms in coastal wetlands.

Effects of conversion of natural forest to plantations on the abundance of nitrite reducing genes in soil aggregates in subtropical forest region.

Large proportion of natural forest has been transformed into plantations in subtropical regions, with consequences on forest ecosystem structure and function. In order to understand the responses of two nitrite reducing genes (nirK and nirS) in N2O production to forest conversion, we collected soil samples from Castanopsis carlesii natural forest, Cunninghamia lanceolata plantation and Pinus massoniana plantation and examined the abundance of nirK and nirS genes in soils and aggregates. Results showed that forest conversion increased soil pH, while decreased soil ammonium content. Forest conversion did not influence the mass proportion of soil aggregates. The abundance of nirK and nirS genes varied in aggregates with different particle sizes. The abundance of nirK and nirS genes was the highest in small macraoaggregates and the lowest in the silt-clay particles. Moreover, the abundance of nirK was significantly higher than that of nirS in soils of all forest types, indicating that nirK dominated in the acidic forest soils. Conversion of natural forest to plantations significantly increased the abundance of nirK and nirS genes in the bulk soil and aggregates, indicating that forest conversion would be beneficial for the growth of microorganisms bearing nirK and nirS genes, which might be associated with the increases of soil pH. Taken together, conversion of natural forest to C. lanceolata plantation or P. massoniana plantation significantly increased the abundance of nirK and nirS in soils and aggregates, but did not affect the mass proportions of aggregates.

Non-native Plant Species Invasion Increases the Importance of Deterministic Processes in Fungal Community Assembly in a Coastal Wetland.

Fungal communities are essential to the maintenance of soil multifunctionality. Plant invasion represents a growing challenge for the conservation of soil biodiversity across the globe, but the impact of non-native species invasion on fungal diversity, community structure, and assembly processes remains largely unknown. Here, we examined the diversity, community composition, functional guilds, and assembly process of fungi at three soil depths underneath a native species, three non-native species, and a bare tidal flat from a coastal wetland. Plant species was more important than soil depth in regulating the diversity, community structure, and functional groups of fungi. Non-native species, especially Spartina alterniflora, increased fungal diversity, altered fungal community structure, and increased the relative abundance of saprotrophic and pathogenic fungi in coastal wetland soils. Stochastic processes played a predominant role in driving fungal community assembly, explaining more than 70% of the relative contributions. However, compared to a native species, non-native species, especially S. alterniflora, reduced the relative influence of stochastic processes in fungal community assembly. Collectively, our results provide novel evidence that non-native species can increase fungal diversity, the relative abundance of saprotrophic and pathogenic fungi, and deterministic processes in the assembly of fungi in coastal wetlands, which can expand our knowledge of the dynamics of fungal communities in subtropical coastal wetlands.

Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland.

Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.

Transcriptome analysis reveals molecular mechanisms underlying salt tolerance in halophyte Sesuvium portulacastrum.

Soil salinity is an important environmental problem that seriously affects plant growth and crop productivity. Phytoremediation is a cost-effective solution for reducing soil salinity and potentially converting the soils for crop production. Sesuvium portulacastrum is a typical halophyte which can grow at high salt concentrations. In order to explore the salt tolerance mechanism of S. portulacastrum, rooted cuttings were grown in a hydroponic culture containing ½ Hoagland solution with or without addition of 400 mM Na for 21 days. Root and leaf samples were taken 1 h and 21 days after Na treatment, and RNA-Seq was used to analyze transcript differences in roots and leaves of the Na-treated and control plants. A large number of differentially expressed genes (DEGs) were identified in the roots and leaves of plants grown under salt stress. Several key pathways related to salt tolerance were identified through KEGG analysis. Combined with physiological data and expression analysis, it appeared that cyclic nucleotide gated channels (CNGCs) were implicated in Na uptake and Na+/H+ exchangers (NHXs) were responsible for the extrusion and sequestration of Na, which facilitated a balance between Na+ and K+ in S. portulacastrum under salt stress. Soluble sugar and proline were identified as important osmoprotectant in salt-stressed S. portulacastrum plants. Glutathione metabolism played an important role in scavenging reactive oxygen species. Results from this study show that S. portulacastrum as a halophytic species possesses a suite of mechanisms for accumulating and tolerating a high level of Na; thus, it could be a valuable plant species used for phytoremediation of saline soils.

Manure applications alter the abundance, community structure and assembly process of diazotrophs in an acidic Ultisol.

The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of α-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9 Mg ha-1) application, rather than medium-rate (18 Mg ha-1) and high-rate (27 Mg ha-1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols.

[Responses of soil ammonia-oxidizing microorganisms to simulated nitrogen deposition in a natural Castanopsis carlesii forest]. / äºšçƒ­å¸¦ç±³æ§ å¤©ç„¶æž—åœŸå£¤æ°¨æ°§åŒ–å¾®ç”Ÿç‰©å¯¹æ¨¡æ‹Ÿæ°®æ²‰é™çš„å“åº”.

Subtropical region of China is one of the global hotspots receiving nitrogen deposition. Nitrogen deposition could affect the abundance and community structure of ammonia oxidizers including ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox Nitrospira), with consequences on soil nutrient cycling that are driven by microorganisms. There is limited understanding for the newly discovered comammox Nitrospira in the subtropical forest soils. Here, we investigated the effect of simulated N deposition on abundances of soil ammonia oxidizers in the Castanopsis fargesii Nature Reserve in Xinkou Town, Sanming City, Fujian Province, China. Soil samples were collected from the field plots which received long-term nitrogen deposition with different dosages, including: CK, no additional treatment; LN, low nitrogen deposition treatment, dosage of 40 kg N·hm-2·a-1; and HN, high nitrogen deposition treatment, dosage of 80 kg N·hm-2·a-1. After 8-year treatment, simulated N deposition decreased soil pH and organic matter content, and increased nitrate content. We failed to amplify the amoA gene of AOB in the tested soils. High nitrogen deposition increased the abundance of AOA, but did not affect the abundance of comammox Nitrospira clade A and clade B. The ratio of comammox Nitrospira to AOA decreased with N addition, indicating that N addition weakened the role of comammox Nitrospira in nitrification in the subtropical forest soils. However, there were strong non-specific amplifications for both comammox Nitrospira clades A and B, highlighting the demand for the development of high coverage and specificity primers for comammox Nitrospira investigations in the future. The abundance of comammox Nitrospira clade A was positively correlated with total nitrogen (TN) and NH4+ concentration, while that of clade B was positively associated with soil organic carbon (SOC), TN and NH4+ Concentration. Overall, our findings demonstrated that simulated N deposition increased the relative importance of AOA in nitrification in the natural Castanopsis carlesii forest soil. These findings could provide theoretical support in coping with global change and N deposition in these regions.

Spartina alterniflora invasion has a greater impact than non-native species, Phragmites australis and Kandelia obovata, on the bacterial community assemblages in an estuarine wetland.

The invasion of Spartina alterniflora poses a serious threat to the sustainability of native ecosystems worldwide. However, compared with other non-native plants (e.g., Phragmites australis and Kandelia obovata), how Spartina alterniflora invasion influences the community structure of bacteria and their assembly processes and functionality remains elusive. Here, we characterized the diversity, community structure, assembly processes and functional guilds of bacteria underneath five plant species and a bare tidal flat at three soil depths in an estuarine wetland. We found that plant species played a more important role than soil depth in mediating the bacterial community structure. Compared with bare tidal flats, the native species Cyperus malaccensis, rather than Scirpus triqueter, significantly changed the bacterial community structure. However, S. alterniflora invasion increased bacterial alpha diversity and significantly altered the bacterial community structure by enriching Chloroflexi, Bacteroidetes and Firmicutes while reducing Acidobacteria, Nitrospirae and Gemmatimonadetes. The invasion of P. australis and translocation of K. obovata had less pronounced effects on the bacterial community structure. Total carbon, total nitrogen and salinity were the key environmental factors mediating the bacterial community structure. Overall of all the non-native plant species, the invasion of S. alterniflora increased the relative importance of stochastic processes in the assembly of bacterial communities, and shifted the bacterial functional profiles by stimulating sulfur cycling groups and suppressing nitrogen cycling groups. Altogether, our results suggest that S. alterniflora invasion has a greater effect than P. australis invasion or K. obovata translocation on the profiles and assembly processes of the bacterial communities, with important implications for soil biogeochemical processes in coastal wetlands.

Divergent responses of wetland methane emissions to elevated atmospheric CO2 dependent on water table.

Elevated atmospheric CO2 may have consequences for methane (CH4) emissions from wetlands, yet the magnitude and direction remain unpredictable, because the associated mechanisms have not been fully investigated. Here, we established an in situ macrocosm experiment to compare the effects of elevated CO2 (700 ppm) on the CH4 emissions from two wetlands: an intermittently inundated Calamagrostis angustifolia marsh and a permanently inundated Carex lasiocarpa marsh. The elevated CO2 increased CH4 emissions by 27.6-57.6% in the C. angustifolia marsh, compared to a reduction of 18.7-23.5% in the C. lasiocarpa marsh. The CO2-induced increase in CH4 emissions from the C. angustifolia marsh was paralleled with (1) increased dissolved organic carbon (DOC) released from plant photosynthesis and (2) reduced (rate of) CH4 oxidation due to a putative shift in methanotrophic community composition. In contrast, the CO2-induced decrease in CH4 emissions from the C. lasiocarpa marsh was associated with the increases in soil redox potential and pmoA gene abundance. We synthesized data from worldwide wetland ecosystems, and found that the responses of CH4 emissions to elevated CO2 was determined by the wetland water table levels and associated plant oxygen secretion capacity. In conditions with elevated CO2, plants with a high oxygen secretion capacity suppress CH4 emissions while plants with low oxygen secretion capacity stimulate CH4 emissions; both effects are mediated via a feedback loop involving shifts in activities of methanogens and methanotrophs.

[Long-term effects of imbalanced fertilization with lime and gypsum additions on denitrifying functional genes of an Ultisol at Yingtan, Jiangxi, China]. / é•¿æœŸç¼ºç´ æ–½è‚¥åŠçŸ³ç°çŸ³è†æ–½ç”¨å¯¹æ±Ÿè¥¿é¹°æ½­çº¢å£¤åç¡åŒ–å¾®ç”Ÿç‰©åŠŸèƒ½åŸºå› ä¸°åº¦çš„å½±å“.

The abundance of denitrifying functional genes plays a key role in driving the soil nitrous oxide (N2O) emission potential. Nitrite reductase genes (nirK and nirS) and nitrous oxide reductase genes (nosZ I and nosZ II) are the dominant denitrifying funtional genes. In this study, real-time quantitative PCR was conducted to evaluate the effects of 32-year imbalanced fertilization and lime and gypsum additions on the abundances of nirK, nirS, nosZ I and nosZ II genes in an Ultisol at Yingtan, Jiangxi Province. We further explored the underlying driving factors. The results showed that, compared with the balanced fertilization treatment, fertilization without phosphorus (P) signifi-cantly decreased the abundances of nirK, nirS, nosZ I and nosZ II genes. Fertilization without nitrogen (N) significantly reduced the abundances of nirK, nosZ I and nosZ II, but did not affect the abundance of nirS. Fertilization without potassium (K) did not affect the abundances of all denitri-fying functional genes. Results of stepwise regression analysis and random forest analysis showed that soil pH was a key environmental factor affecting the abundances of nosZ I and nosZ II. The application of lime or lime + gypsum significantly increased soil pH, which subsequently increased the abundances of nosZ II and nosZ II/nosZ I by 150%-231% and 127%-155%, respectively. Our results suggested that application of lime or lime + gypsum favored nosZ II more than nosZ I in upland Ultisols, which might enhance the relative importance of nosZ II in N2O reduction. Overall, fertilization without P would reduce denitrifying gene abundances, while the application of lime or lime + gypsum enriched nosZ II and increased ratio of nosZ II/nosZ I, which might be beneficial for reducing N2O emission potential in the Ultisols.

[Responses of denitrifying functional gene abundance to long-term fertilization regimes in an upland Ultisol]. / æ—±åœ°çº¢å£¤åç¡åŒ–åŠŸèƒ½åŸºå› ä¸°åº¦å¯¹é•¿æœŸæ–½è‚¥çš„å“åº”.

Fertilization affects soil nitrogen cycling and nitrous oxide (N2O) emissions, which are mainly driven by microbes. A 32-year field experiment was conducted to investigate the effects of chemical fertilizers and their combination with organic materials on the abundance of denitrifying functional genes (nirS, nirK, nosZ I and nosZ II) in Ultisol. The treatments comprised no fertilizer (CK), chemical fertilizer, chemical fertilizer+peanut straw, chemical fertilizer+rice straw, chemical fertilizer+radish and chemical fertilizer+pig manure. Compared with the single chemical fertilizer treatment, soil pH and organic carbon content increased in the chemical fertilizer plus organic material treatments, with chemical fertilizer+pig manure having the strongest effect. Long-term fertilization did not affect the abundance of nirK gene, but significantly altered the nirS gene abundance. Compared to CK, long-term chemical fertilizer application increased the abundance of nirS gene by 426%. However, partial replacement of chemical fertilizer by organic materials decreased the abundance of nirS gene. The abundance of nosZ I gene was one order of magnitude higher than that of nosZ II, indicating the domination of nosZ I in the acidic Ultisol. Long-term fertilization did not affect the abundance of nosZ II, whereas chemical fertilizer+pig manure increased the abundance of nosZ I by 138%. Results of stepwise regression analysis showed that available phosphorus content was the primary factor regulating the abundance of nosZ I gene, whereas the abundance of the nosZ II gene was mainly regulated by nitrate content. Moreover, the lowest (nirS+nirK)/(nosZ I+nosZ II) value in the chemical fertilizer+pig manure treatment indicated that long-term manure application might reduce N2O emission potential in Ultisols.

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization.

Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO3) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the Nitrososphaera and B1 clades but shifted to clade A in the NL and NPM treatments. Nitrosospira cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of Nitrosospira cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that Nitrosospira cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization.IMPORTANCE The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. Nitrosospira cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.

Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO2.

The effects of elevated atmospheric CO2 concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO2 in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO2 (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO2 increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO2. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO2. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO2.

Effect of application of dairy manure, effluent and inorganic fertilizer on nitrogen leaching in clayey fluvo-aquic soil: A lysimeter study.

Dairy farm manure and effluent are applied to cropland in China to provide a source of plant nutrients, but there are concerns over its effect on nitrogen (N) leaching loss and groundwater quality. To investigate the effects of land application of dairy manure and effluent on potential N leaching loss, two lysimeter trials were set up in clayey fluvo-aquic soil in a winter wheat-summer maize rotation cropping system on the North China Plain. The solid dairy manure trial included control without N fertilization (CK), inorganic N fertilizer (SNPK), and fresh (RAW) and composted (COM) dairy manure. The liquid dairy effluent trial consisted of control without N fertilization (CF), inorganic N fertilizer (ENPK), and fresh (FDE) and stored (SDE) dairy effluent. The N application rate was 225kgNha-1 for inorganic N fertilizer, dairy manure, and effluent treatments in both seasons. Annual N leaching loss (ANLL) was highest in SNPK (53.02 and 16.21kgNha-1 in 2013/2014 and 2014/2015, respectively), which were 1.65- and 2.04-fold that of COM, and 1.59- and 1.26-fold that of RAW. In the effluent trial (2014/2015), ANLL for ENPK and SDE (16.22 and 16.86kgNha-1, respectively) were significantly higher than CF and FDE (6.3 and 13.21kgNha-1, respectively). NO3- contributed the most (34-92%) to total N leaching loss among all treatments, followed by dissolved organic N (14-57%). COM showed the lowest N leaching loss due to a reduction in NO3- loss. Yield-scaled N leaching in COM (0.35kgNMg-1 silage) was significantly (P<0.05) lower than that in the other fertilization treatments. Therefore, the use of composted dairy manure should be increased and that of inorganic fertilizer decreased to reduce N leaching loss while ensuring high crop yield in the North China Plain.