Soil organic matter and salinity as critical factors affecting the bacterial community and function of Phragmites australis dominated riparian and coastal wetlands

Intensive ammonium fertilizer addition activates iron and carbon conversion coupled cadmium redistribution in a paddy soil under gradient redox conditions

While over-fertilization and nitrogen deposition can lead to the enrichment of nitrogen in soil, its effects on heavy metal fractions under gradient moisture conditions remains unclear. Here, the effect of intensive ammonium (NH4+) addition on the conversion and interaction of cadmium (Cd), iron (Fe) and carbon (C) was studied. At relatively low (30-80 %) water hold capacity (WHC) NH4+ application increased the carbonate bound Cd fraction (F2Cd), while at relatively high (80-100 %) WHC NH4+ application increased the organic matter bound Cd fraction (F4Cd). Iron‑manganese oxide bound Cd fractions (F3Cd) and oxalate-Fe decreased, but DCB-Fe increased in NH4+ treatments, indicating that amorphous Fe was the main carrier of F3Cd. The variations in F1Cd and F4Cd observed under the 100-30-100 % WHC treatment were similar to those observed under low moisture conditions (30-60 % WHC). The C=O/C-H ratio of organic matter in soil decreased under the 30-60 % WHC treatment, but increased under the 80-100 % WHC treatment, which was the dominant factor influencing F4Cd changes. The conversion of NH4+ declined with increasing soil moisture content, and the impact on oxalate-Fe was greater at 30-60 % WHC than at 80-100 % WHC. Correspondingly, genetic analysis showed the effect of NH4+ on Fe and C metabolism at 30-60 % WHC was greater than at 80-100 % WHC. Specifically, NH4+ treatment enhanced the expression of genes encoding extracellular Fe complexation (siderophore) at 30-80 % WHC, while inhibiting genes encoding Fe transmembrane transport at 30-60 % WHC, indicating that siderophores simultaneously facilitated Cd detoxification and Fe complexation. Furthermore, biosynthesis of sesquiterpenoid, steroid, butirosin and neomycin was significantly correlated with F4Cd, while glycosaminoglycan degradation metabolism and assimilatory nitrate reduction was significantly correlated with F2Cd. Overall, this study gives a more comprehensive insight into the effect of NH4+ on activated Fe and C conversion on soil Cd redistribution under gradient moisture conditions.

Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands

Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.

Kalidium cuspidatum colonization changes the structure and function of salt crust microbial communities

The changes of soil moisture, salinity, and nutrients by halophyte colonization in high-salinity environment profoundly affect the assembly and structure of microbial communities. However, salt marshes in arid region have received little attention. This study was conducted in Lianhuachi Lake, a typical inland salt marsh wetland in China, to determine the physicochemical characteristics of salt crusts in [Kalidium cuspidatum (Ung.-Sternb.) Grub.] colonization areas and bulk soil, respectively, and to analyze the microbial community structure of salt crusts by high-throughput sequencing. Kalidium cuspidatum colonization significantly decreased total salinity, soil water content, and water-soluble ions of salt crusts and increased total carbon, total nitrogen, and total phosphorus content. At the same time, changes in physicochemical properties caused by Kalidium cuspidatum colonization affect the ecological processes of bacterial, fungal, and archaeal community assemblies in salt crusts. In addition, cross-kingdom network analysis showed that Kalidium cuspidatum colonization increased the complexity and stability of microbial networks in salt crust soils. Functional projections further showed that bacterial diversity had a potential driving effect on the nitrogen cycle function of salt crust. Our study further demonstrated the different ecological strategies of microorganisms for halophyte colonization in extreme environments and contributed to the understanding of restoration and management of salt marsh wetlands in arid region.

Deep groundwater irrigation altered microbial community and increased anammox and methane oxidation in paddy wetlands of Sanjiang Plain, China

The over-utilizing of nitrogen fertilizers in paddy wetlands potentially threatens to the surrounding waterbody, and a deep understanding of the community and function of microorganisms is crucial for paddy non-point source pollution control. In this study, top soil samples (0-15 cm) of paddy wetlands under groundwater's irrigation at different depths (H1: 6.8 m, H2: 13.7 m, H3: 14.8 m, H4: 15.6 m, H5: 17.0 m, and H6: 17.8 m) were collected to investigate microbial community and function differences and their interrelation with soil properties. Results suggested some soil factor differences for groundwater's irrigation at different depths. Deep-groundwater's irrigation (H2-H6) was beneficial to the accumulation of various electron acceptors. Nitrifying-bacteria Ellin6067 had high abundance under deep groundwater irrigation, which was consistent with its diverse metabolic capacity. Meanwhile, denitrifying bacteria had diverse distribution patterns. Iron-reducing bacteria Geobacter was abundant in H1, and Anaeromyxobacter was abundant under deep groundwater irrigation; both species could participate in Fe-anammox. Furthermore, Geobacter could perform dissimilatory nitrate reduction to ammonia using divalent iron and provide substrate supply for anammox. Intrasporangium and norank_f_Gemmatimonadacea had good chromium- and vanadium-reducting potentials and could promote the occurrence of anammox. Low abundances of methanotrophs Methylocystis and norank_f_Methyloligellaceae were associated with the relatively anoxic environment of paddy wetlands, and the presence of aerobic methane oxidation was favorable for in-situ methane abatement. Moisture, pH, and TP had crucial effects on microbial community under phylum- and genus-levels. Microorganisms under shallow groundwater irrigation were highly sensitive to environmental changes, and Fe-anammox, nitrification, and methane oxidation were favorable under deep groundwater irrigation. This study highlights the importance of comprehensively revealing the microbial community and function of paddy wetlands under groundwater's irrigation and reveals the underlying function of indigenous microorganisms in agricultural non-point pollution control and greenhouse gas abatement.

Arbuscular mycorrhizal fungi increased peanut (Arachis hypogaea L.) yield by changing the rhizosphere microbial community structure in saline-alkali soil

Arbuscular mycorrhizal fungi (AMF) have demonstrated the potential to enhance the saline-alkali tolerance in plants. Nevertheless, the extent to which AMF can ameliorate the tolerance of salt-sensitive plants to alkaline conditions necessitates further investigation. The current study is primarily centered on elucidating the impact of AMF on the growth of the Huayu22 (H22) when cultivated in saline-alkaline soil. We leveraged DNA of rhizosphere microorganisms extracted from saline-alkali soil subjected to AMF treatment and conducted high-throughput sequencing encompassing 16S rRNA gene and ITS sequencing. Our findings from high-throughput sequencing unveiled Proteobacteria and Bacillus as the prevailing phylum and genus within the bacterial population, respectively. Likewise, the predominant fungal phylum and genus were identified as Ascomycota and Haematonectria. It is noteworthy that the relative abundance of Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, and Ascomycota exhibited significant increments subsequent to AMF inoculation. Our investigation into soil enzyme activity revealed a remarkable surge post-AMF inoculation. Notably, the amounts of pathogen growth inhibitory enzymes and organic carbon degrading enzymes rise, as predicted by the putative roles of microbial communities. In saline-alkali soil, inoculation of AMF did boost the yield of H22. Notable improvements were observed in the weight of both 100 fruits and 100 grains, which increased by 20.02% and 22.30%, respectively. Conclusively, this study not only provides a theoretical framework but also furnishes empirical evidence supporting the utilization of AMF as a viable strategy for augmenting the yield of salt-sensitive plants grown in alkaline conditions.

Blue carbon benefits from global saltmarsh restoration

Coastal saltmarshes are found globally, yet are 25%-50% reduced compared with their historical cover. Restoration is incentivised by the promise that marshes are efficient storers of 'blue' carbon, although the claim lacks substantiation across global contexts. We synthesised data from 431 studies to quantify the benefits of saltmarsh restoration to carbon accumulation and greenhouse gas uptake. The results showed global marshes store approximately 1.41-2.44 Pg carbon. Restored marshes had very low greenhouse gas (GHG) fluxes and rapid carbon accumulation, resulting in a mean net accumulation rate of 64.70 t CO2 e ha-1 year-1 . Using this estimate and potential restoration rates, we find saltmarsh regeneration could result in 12.93-207.03 Mt CO2 e accumulation per year, offsetting the equivalent of up to 0.51% global energy-related CO2 emissions-a substantial amount, considering marshes represent <1% of Earth's surface. Carbon accumulation rates and GHG fluxes varied contextually with temperature, rainfall and dominant vegetation, with the eastern coasts of the USA and Australia particular hotspots for carbon storage. While the study reveals paucity of data for some variables and continents, suggesting need for further research, the potential for saltmarsh restoration to offset carbon emissions is clear. The ability to facilitate natural carbon accumulation by saltmarshes now rests principally on the action of the management-policy community and on financial opportunities for supporting restoration.

Effects of chromate on nitrogen removal and microbial community in two-stage vertical-flow constructed wetlands

Nitrogen and chromium (Cr(VI)) pollution in waterbodies pose great threats to human health, and a cost-effective alternative with Cr(VI) and nitrogen simultaneous removal is still needed. This study investigated the influence of Cr(VI) on nitrogen removal in the two-stage vertical-flow constructed wetlands (TS-VFCWs) along with iron ore and woodchip, and explored relationship between Cr(VI) and nitrogen removal. The results showed that efficient Cr(VI) and nitrogen removal were simultaneously achieved in TS-VFCWs together with iron-ore and woodchip under 2 mg/L-Cr(VI), whereas 10 mg/L-Cr(VI) gave significant and recoverable inhibition of nitrogen removal. Cr(VI) supplementation promoted the beneficiation of Cr(VI)-reducing/resistant bacteria IMCC26207 and Bryobacter on iron-ore. Woodchip enriched Cr(VI)-reducing bacteria Streptomyces and Thiobacillus. XRD and XPS showed that abundant bound-Cr existed in the surface of iron ore and woodchip, and Cr(III) precipitation/oxide was the major product. High abundances of nitrifying and autotrophic/heterotrophic denitrifying bacteria ensured good nitrogen removal at Cr(VI) stress.

Niche differentiation and influencing factors of nitrite oxidation bacteria Nitrospira in sediments of the Luan River estuary in China

In the estuarine sediment, the nitrite oxidation process mediated by bacteria significantly influences nitrification. Nitrospira is the most widely distributed nitrite-oxidizing bacteria (NOB) and can adapt to various environments. In this study, the Nitrospira-specific primer nxrB 169F-638R was used to analyze the microbial communities in the sediments of low-, middle-, and high-level zones in the Luan River estuary. The structure of the microbial community and its response to environmental factors were also assessed. The abundance and diversity of Nitrospira were the highest in the low-level zone and lowest in the high-level zone. Lineage II and lineage IV were the dominant Nitrospira at 43.58% and 32.09%, respectively. The distribution pattern of Nitrospira was also affected by complex environmental factors, such as the concentration of NH4+, Fe, and Cu cations. This study provides novel insights into the niche differentiation and adaptation strategies of Nitrospira in an estuarine sediment environment and will help to facilitate single-step nitrification.

Stronger effects of simultaneous warming and precipitation increase than the individual factor on soil bacterial community composition and assembly processes in an alpine grassland

Composition and traits of soil microbial communities that closely related to their ecological functions received extensive attention in the context of climate changes. We investigated the responses of soil bacterial community structure, traits, and functional genes to the individual warming, precipitation increases, and the combination of warming and precipitation increases in an alpine grassland in the Qinghai-Tibet Plateau that is experiencing warming and wetting climate change. Soil properties, plant diversity and biomass were measured, and the ecological processes and environmental factors driving bacterial community changes were further explored. Results indicated that the Shannon diversity of soil bacterial communities decreased significantly only under the combination treatment, which might due to the decreased plant diversity. Soil bacterial community composition was significantly correlated with soil pH, and was affected obviously by the combination treatment. At the taxonomic classification, the relative abundance of Xanthobacteraceae and Beijerinckiaceae increased 127.67 and 107.62%, while the relative abundance of Rubrobacteriaceae and Micromonosporaceae decreased 78.29 and 54.72% under the combination treatment. Functional genes related to nitrogen and phosphorus transformation were enhanced in the combination treatment. Furthermore, weighted mean ribosomal operon copy numbers that positively correlated with plant aboveground biomass increased remarkably in the combination treatment, indicating a trend of life-history strategies shift from oligotrophic to copiotrophic. Stochastic processes dominated soil bacterial community, and the proportion of stochasticity increased under the combination treatment. Our study highlights the significant effects of simultaneous warming and precipitation increase on soil bacterial community.

Root architectures differentiate the composition of organic carbon in bauxite residue during natural vegetation

Understanding plant root architectures induced changes in organic carbon accumulation and conversion is critical to predicting carbon cycling and screening appropriate plant species for ecological restoration on bauxite residue disposal areas. According to the ecological investigation of a weathered bauxite residue disposal area, three plants with different root architectures including Artemisia lavandulaefolia (A. lavandulaefolia), moss, and Zanthoxylum simulans (Z. simulans) were selected to investigate the rhizosphere effects on the composition and structure of organic carbon in bauxite residue. The physic-chemical properties, the contents and structure of different organic carbon fractions, and microbial communities of bauxite residue from rhizosphere and non-rhizosphere were analyzed. Plant growth decreased the saline-alkalinity, increased the contents of total organic carbon, particulate organic carbon and dissolved organic carbon, whilst enhancing the enzymatic activities of bauxite residue. Meanwhile, the rhizosphere effects had significant effects on the accumulation and stabilization of organic carbon in bauxite residue. A. lavandulaefolia had the strongest rhizosphere effects on the composition and structure of total organic carbon and dissolved organic carbon, whilst moss was more effective on the accumulation of particulate organic carbon in bauxite residue. Plant growth and root architecture changed the abundance of specific functional microorganisms and the complexity of microbial co-occurrence networks, thus elevating organic carbon levels in bauxite residue. During natural vegetation encroachment, rhizosphere exciting effects of the salt-tolerated plants could change the composition and structure of organic carbon fractions due to the comprehensive effectiveness of the improvement of physic-chemical properties and microbial communities. The findings improve our understanding of the responses of sequestration and stabilization of organic carbon pools to ecological restoration on bauxite residue disposal areas.

Microorganisms in coastal wetland sediments: a review on microbial community structure, functional gene, and environmental potential

Coastal wetlands (CW) are the junction of the terrestrial and marine ecosystems and have special ecological compositions and functions, which are important for maintaining biogeochemical cycles. Microorganisms inhabiting in sediments play key roles in the material cycle of CW. Due to the variable environment of CW and the fact that most CW are affected by human activities and climate change, CW are severely degraded. In-depth understanding of the community structure, function, and environmental potential of microorganisms in CW sediments is essential for wetland restoration and function enhancement. Therefore, this paper summarizes microbial community structure and its influencing factors, discusses the change patterns of microbial functional genes, reveals the potential environmental functions of microorganisms, and further proposes future prospects about CW studies. These results provide some important references for promoting the application of microorganisms in material cycling and pollution remediation of CW.

Response of microbial community in the soil of halophyte after contamination with tetrabromobisphenol A

Coastal wetlands are subjected to increasing tetrabromobisphenol A (TBBPA) pollution, whereas knowledge of TBBPA degradation in marine environments is lacking. The changes of bacterial communities in TBBPA-polluted soil covered with halophytes were investigated. TBBPA could be degraded in the halophyte-covered saline-alkali soil in a microcosm experiment. Higher TBBPA removal occurred in the soil of Kandelia obovata compared with soils covered with Suaeda australis and Phragmites australis within 56 days of cultivation. The rhizosphere soils of S. australis, P. australis, and K. obovata mainly involved the classes of Bacteroidia, Gammaproteobacteria, Alphaproteobacteria, and Anaerolineae. Additionally, manganese oxidation, aerobic anoxygenic phototrophy, and fermentation functions were higher in the rhizosphere soil of K. obovata after TBBPA addition. This study supports that using suitable local halophytic plants is a promising approach for degrading TBBPA-contaminated coastal soil.

Global patterns and edaphic-climatic controls of soil carbon decomposition kinetics predicted from incubation experiments

Knowledge about global patterns of the decomposition kinetics of distinct soil organic matter (SOM) pools is crucial to robust estimates of land-atmosphere carbon fluxes under climate change. However, the current Earth system models often adopt globally-consistent reference SOM decomposition rates (k_ref), ignoring effects from edaphic-climate heterogeneity. Here, we compile a comprehensive set of edaphic-climatic and SOM decomposition data from published incubation experiments and employ machine-learning techniques to develop models capable of predicting the expected sizes and k_ref of multiple SOM pools (fast, slow, and passive). We show that soil texture dominates the turnover of the fast pools, whereas pH predominantly regulates passive SOM decomposition. This suggests that pH-sensitive bacterial decomposers might have larger effects on stable SOM decomposition than previously believed. Using these predictive models, we provide a 1-km resolution global-scale dataset of the sizes and k_ref of these SOM pools, which may improve global biogeochemical model parameterization and predictions.

Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.

Soil salinity, not plant genotype or geographical distance, shapes soil microbial community of a reed wetland at a fine scale in the Yellow River Delta

Soil salinization is one of the most severe environmental problems restricting biodiversity maintenance and ecosystem functioning in a coastal wetland. Recent studies have well documented how salinization affects soil microbial communities along vegetation succession of coastal wetlands. However, the salinity effect is rarely assessed in the context of plant intraspecific variation. Here, we analyzed the soil bacterial and fungal communities of Phragmites australis wetland using amplicon high-throughput sequencing at a fine scale (within 1000 m) in the Yellow River Delta. Our results revealed that microbial diversity is significantly correlated to soil salinity (assessed as electrical conductivity, EC) but not to soil nutrients (N and P content) or plant intraspecific traits (leaf length, shoot height, and neutral genetic variation). Specifically, the microbial diversity tended to decrease with increased EC, and the bacterial community was more sensitive to EC change than the fungal community. The dominant bacterial phyla were Proteobacteria, Actinobacteria, and Chloroflexi, and the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. The relative abundance of Actinobacteria was significantly negatively correlated to EC, while Proteobacteria were positively correlated to EC. In high salinity (> 1 mS/cm), the role of the stochastic processes became more important in community assembly according to habitat niche breadth estimation, neutral community model, C-score metric, and normalized stochasticity ratio. Additional common garden and microcosm experiments provided evidence that the genotype effect of P. australis on soil microbiome might only occur between lineages from different regions but not from the same region like the Yellow River Delta. Our findings provide new insights into soil microbial community assembly processes with the intraspecific variation of host plants in the wetland ecosystem and offer a scientific reference for salinity mitigation and vegetation management of coastal wetlands under future global changes.

Prediction of Soil Water-Soluble Organic Matter by Continuous Use of Corn Biochar Using Three-Dimensional Fluorescence Spectra and Deep Learning

The purpose is to study the soil's water-soluble organic matter and improve the utilization rate of the soil layer. This exploration is based on the theories of three-dimensional fluorescence spectroscopy, deep learning, and biochar. Chernozem in Harbin City, Heilongjiang Province, is taken as the research object. Three-dimensional fluorescence spectra and a deep learning model are used to analyze the content of water-soluble organic matter in the soil layer after continuous application of corn biochar for six years and to calculate different fluorescence indexes in the whole soil depth. Among them, the three-dimensional fluorescence spectrum theory provides the detection standard for the application effect detection of biochar, the deep learning theory provides the technical support for this exploration, and the biochar theory provides the specific research direction. The results show that the application of corn biochar for six consecutive years significantly reduces the average content of water-soluble organic matter in different soil layers. Among them, the highest average content of soil water-soluble organic matter is "nitrogen, potassium, phosphorous" (NPK) and the lowest is "boron, carbon" (BC). Comparing the soil with BC alone, in the topsoil, the second section (330-380 nm/200-250 nm) with BC + NPK increases by 13.3%, the third section (380-550 nm/220-250 nm) increases by 8.4%, and the fourth section (250-380 nm/250-600 nm) increases by 50.1%. The combination of nitrogen (N) + BC has a positive effect of 20.7%, 12.2%, and 28.4% on sections I, II, and IV, respectively. In addition, in the topsoil, the combination of NPK + BC significantly increases the content of acid-like substances compared with the application of BC alone. In the black soil, with or without fertilizer NPK, there is no significant difference in the level of fulvic acid-like components. The prediction of soil water-soluble organic matter after continuous application of corn biochar based on three-dimensional fluorescence spectra and deep learning is carried out, which has reference significance for the rapid identification and early prediction of subsequent soil activity.

Changes in the composition of rhizosphere bacterial communities in response to soil types and acid rain

It is widely known how acid rain negatively impacts plant physiology. However, the magnitude of these effects may depend on soil types. Although the response of aboveground parts has received much attention, the effects of soil types and acid rain on underground processes are yet to be studied, specifically with respect to the composition and diversity of bacterial communities in the rhizosphere. Based on a high throughput sequencing approach, this study examined how different soil types, acid rain of different pH, and interactions between the two factors influenced the growth and rhizosphere bacterial communities of Jatropha curcas L. The present study pointed out that the soil pH, total nitrogen (TN), total phosphorus (TP), total potassium (TK), and total organic carbon/total nitrogen (C/N) were more related to soil type than to acid rain. The growth of J. curcas aboveground was mainly affected by acid rain, while the underground growth was mainly influenced by soil type. Changes in bacterial abundance indicated that the genera (Burkholderia-Paraburkholde, Bryobacter, Cupriavidus, Mycobacterium, and Leptospirillu) and phyla (Acidobacteria and Actinobacteria) could likely resist acid rain to some extent, with Acidobacteria, Gemmatimonadetes and Proteobacteria being well adapted to the copiotrophic environments. Results of correlational analyses between Firmicutes and soil properties (pH, TN, TK) further indicated that this phylum was also well adapted to a nutrient-deficient habitat of low pH. Finally, while Mycobacterium and Bradyrhizobium could adapt to low pH, high soil TK contents were not conducive to their enrichment. The results also showed that acid rain shifted the bacterial groups from fast-growing copiotrophic populations to slow-growing oligotrophic ones. The RDA analysis, and Pearson's rank correlation coefficients indicated that soil pH and TK were the main factors influencing bacterial richness.

Unveiling microbial community and function involved in anammox in paddy vadose under groundwater irrigation

The extensive application of nitrogen fertilizer in intensive irrigation areas poses a potential threat to groundwater. Given that the vadose zone acts as a buffer zone for the underground entry of surface pollutants, an in-depth understanding of its microbial community structure and function was crucial for controlling groundwater nitrogen pollution. In this study, soil samples from paddy vadose under groundwater irrigation with different depths (G1: 6.8 m, G2: 13.7 m, G3: 15.6 m, and G4: 17.8 m) were collected to unravel the differences in microbial community structure and function at different vadose depths (0-250 cm), as well as their relationship with soil properties. Results showed some differences among soil physicochemical factors under groundwater irrigation with different depths and that some electron acceptors were more abundant than others under deep groundwater irrigation (G2-G4). Remarkable differences in microbial communities under shallow- and deep-groundwater irrigation were found. The high abundances of anammox bacteria Candidatus_Brocadia in G2 and G3 indicated that deep groundwater irrigation was beneficial to its enrichment. Iron-reducing bacteria Anaeromyxobacter and sulfate-reducing bacteria Desulfovibrio were widely distributed in vadose zone and possessed the potential for anammox coupled with Fe(III)/sulfate reduction. Norank_f_Gemmatimonadaceae had nitrate- and vanadium-reducing abilities and could participate in anammox in vadose zone. Dissimilatory nitrate reduction to ammonia (DNRA) bacteria Geobacter facilitated Fe(II)-driven DNRA and thus provided electron donors and acceptors to anammox bacteria. Soil nutrients and electron donors/acceptors played important roles in shaping microbial community structure at phylum and genus levels. Microorganisms in vadose zone under groundwater irrigation showed good material/energy metabolism levels. Deep groundwater irrigation was conducive to the occurrence of anammox coupled with multi-electron acceptors. Our findings highlight the importance of understanding the structure and function of microbial communities in paddy vadose under groundwater irrigation and reveal the potential role of indigenous microorganisms in in-situ nitrogen removal.

Impact of Soil Fertilized with Biomass Ash on Depth-Related Variability of Culturable Bacterial Diversity and Selected Physicochemical Parameters in Spring Barley Cultivation

This study investigated the effect of different doses of fertilization with biomass combustion ash (Salix viminalis L. willow) on changes in the biological, chemical, and physical properties of soil. The experiment was carried out on podzolic and chernozem soils in a one-way field experiment (fertilization dose: control (without fertilization), NPK (nitrogen (N), phosphorus (P) and potassium (K)), 100, 200, 300, 400, 500 kg K₂O ha^-1). The biomass ash was characterized by a pH value of 12.83 ± 0.68 and a high content of macronutrients. The samples were collected from 0-5, 10-15, and 20-25 cm soil layers under the cultivation of spring barley (Hordeum vulgare L) cv. Planet in April and August 2021. Mass spectrometry (MALDI-TOF MS) was used for microbiological analyses, which revealed the presence of 53 culturable species from 11 genera: Bacillus, Pseudomonas, Paenibacillus, Lysinibacillus, Pseudarthrobacter, Arthrobacter, Staphylococcus, Paenarthrobacter, Micrococcus, Rhodococcus, and Flavobacterium. The podzolic and chernozem soils exhibited the presence of 28 and 44 culturable species, respectively. The study showed an increase in the number of microorganisms in the top layer of the soil profile. However, the number of bacteria decreased at the depths of 10-15 cm and 20-25 cm. With depth, the bulk density (BD) and moisture increased.

Shifts in Soil Microbial Community Composition, Function, and Co-occurrence Network of Phragmites australis in the Yellow River Delta

Soil microorganisms play vital roles in regulating biogeochemical processes. The composition and function of soil microbial community have been well studied, but little is known about the responses of bacterial and fungal communities to different habitats of the same plant, especially the inter-kingdom co-occurrence pattern including bacteria and fungi. Herein, we used high-throughput sequencing to investigate the bacterial and fungal communities of five Phragmites australis habitats in the Yellow River Delta and constructed their inter-kingdom interaction network by network analysis. The results showed that richness did not differ significantly among habitats for either the bacterial or fungal communities. The distribution of soil bacterial community was significantly affected by soil physicochemical properties, whereas that of the fungal community was not. The main functions of the bacterial and fungal communities were to participate in the degradation of organic matter and element cycling, both of which were significantly affected by soil physicochemical properties. Network analysis revealed that bacteria and fungi participated in the formation of networks through positive interactions; the role of intra-kingdom interactions were more important than inter-kingdom interactions. In addition, rare species acted as keystones played a critical role in maintaining the network structure, while NO3−−N likely played an important role in maintaining the network topological properties. Our findings provided insights into the inter-kingdom microbial co-occurrence network and response of the soil microbial community composition and function to different P. australis habitats in coastal wetlands, which will deepen our insights into microbial community assembly in coastal wetlands.

Remediation of organic amendments on soil salinization: Focusing on the relationship between soil salts and microbial communities

Soil salinization has emerged as a major factor with an adverse influence on agricultural green development worldwide. It is necessary to develop high-efficiency and ecologically beneficial management measures for alleviating soil salinization. The experiment of application for cow manure (CM), biochar (BC), and bio-organic fertilizer (BIO) in soil with light salinity was conducted to investigate the remediation of organic materials on soil salinization with melon (Cucumis melo L.) by reducing the availability of saline ions and shifting the soil microbial community. Results showed that BC treatment significantly decreased the EC values of the soil and soil solution by 19.23% and 27.02% and the concentrations of Na⁺, K⁺, and Cl^- by 13.28%, 13.08%, and 15.21%, respectively, followed by CM and BIO treatments. High-throughput sequencing identified that organic amendments significantly improved the richness of the soil bacterial community and increased the relative abundances of Acidobacteria and Firmicutes by 33.11% and 111.2%, respectively, and the beneficial salt-tolerant bacterial genera Flavobacterium, Bacillus and Arthrobacter by 32.04%, 38.92% and 35.67%, respectively. Additionally, soil Na⁺, Ca²⁺, K⁺ and Cl^- were significantly negatively correlated with Acidobacteria and Flavobacterium and were also the most important factors driving the changes in the structure of the soil bacterial communities. The bacterial networks were more complex in the organic amendments treatments than in CK, reflecting through more nodes and links and a higher average clustering coefficient, density and modularity. This study provided a comprehensive understanding of the application of organic amendments in alleviating soil salinization and improving soil bacterial and fungal communities and provides scientific support for agriculture green development.

Effects of a Furrow-Bed Seeding System on Stand Establishment, Soil Bacterial Diversity, and the Yield and Quality of Alfalfa Under Saline Condition

Salt stress account for large decreases in crop yield all over the world. Furrow-bed system is an efficient practice to promote plant growth in saline soil. However, the effects of Furrow-bed system on the soil environment and the growth of alfalfa (Medicago sativa L.) in salinity are not clear. For a wider and more detail evaluation, alfalfa were planted in saline sandy loam soil in fall, the effects of two plant systems (FU, furrow-bed seeding system; FL, flat-bed seeding system) on soil moisture, root zone salinity, soil microbial community structure, seedling emergence number in the early stage of the growth period and soil nutrient contents, alfalfa production characteristics in the second growth year were determined in a 2-year field experiment. The result showed that, compared with FL, FU resulted in increased soil moisture content and seedling emergence, and significantly reduced relative abundance of Actinobacteria and Choroflexi in soil, but it did not affect root zone salinity at the seedling stage. In April of second growth year, the soil salinity was lower, and the soil available phosphorus, potassium, nitrogen, and soil organic matter contents of the root zone were higher in FU than in FL. Compared with FL, FU resulted in increased yield (by 37.5%), protein content (by 3.6%), and potassium concentration (by 33.2%), and decreased ash content (by 7.7%), and sodium concentration (by 19.0%) in alfalfa plants. Pearson's correlation analysis indicated that the increased yield was positively correlated with seedling emergence, soil available potassium, total nitrogen, and organic matter contents, and shoot potassium content and negatively correlated with shoot sodium content. The relative abundance of Actinobacteria was negatively correlated with alfalfa ash, calcium, and sodium concentrations, and positively correlated with shoot potassium content. Taken together, the results indicate that Furrow-bed seeding in early fall alleviated salt stress of alfalfa and have the potential to enhance the yield and quality of alfalfa cultivated in saline soils by improving the soil environment and regulating the growth and physiology of alfalfa. Graphical Abstract.

Estimation of Soil Salt Content and Organic Matter on Arable Land in the Yellow River Delta by Combining UAV Hyperspectral and Landsat-8 Multispectral Imagery

Rapid and large-scale estimation of soil salt content (SSC) and organic matter (SOM) using multi-source remote sensing is of great significance for the real-time monitoring of arable land quality. In this study, we simultaneously predicted SSC and SOM on arable land in the Yellow River Delta (YRD), based on ground measurement data, unmanned aerial vehicle (UAV) hyperspectral imagery, and Landsat-8 multispectral imagery. The reflectance averaging method was used to resample UAV hyperspectra to simulate the Landsat-8 OLI data (referred to as fitted multispectra). Correlation analyses and the multiple regression method were used to construct SSC and SOM hyperspectral/fitted multispectral estimation models. Then, the best SSC and SOM fitted multispectral estimation models based on UAV images were applied to a reflectance-corrected Landsat-8 image, and SSC and SOM distributions were obtained for the YRD. The estimation results revealed that moderately salinized arable land accounted for the largest proportion of area in the YRD (48.44%), with the SOM of most arable land (60.31%) at medium or lower levels. A significant negative spatial correlation was detected between SSC and SOM in most regions. This study integrates the advantages of UAV hyperspectral and satellite multispectral data, thereby realizing rapid and accurate estimation of SSC and SOM for a large-scale area, which is of great significance for the targeted improvement of arable land in the YRD.

Elaeagnus angustifolia can improve salt-alkali soil and the health level of soil: Emphasizing the driving role of core microbial communities

Saline-alkali environments are widely distributed in China and significantly hinder the development of agriculture. This study characterizes the long-term effects of planting Elaeagnus angustifolia (E. angustifolia) on the physical and chemical properties, enzyme activities and microbial community characteristics of saline-alkali soil in the Songnen Plain (1, 2 and 3 years). The results showed that planting E. angustifolia reduced soil pH and electrical conductivity (EC) and increased soil total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (Nni), total potassium (TK), dissolved organic C (DOC), dissolved organic matter (DOM) and available potassium (AK) content and catalase, urease, polyphenol oxidase, phosphatase, sucrase and cellulase enzyme activities, and the results peaked in the 3 year. High-throughput sequencing showed that the bacterial abundance and diversity were as follows (from high to low) y3 > y2 > y1 > CK. E. angustifolia resulted in an increase in the relative abundance of the dominant bacteria. Proteobacteria and Pseudomonas were the major phylum and genus, respectively. Redundancy analysis showed that changes in the soil microbial community significantly affect the physical and chemical properties of the soil, with Proteobacteria members being the key microorganisms that reduce soil salinity. Network analysis showed that Pseudomonas (Proteobacteria) participated in the synthesis of key soil enzymes. 16S rRNA sequencing predicted that the expression of genes related to carbon (rbcL, acsA, acsB, Pcc and accA) and nitrogen (amoA/B, nxrA, hao, gdh, ureC and nosZ) transformation increased, and Pseudomonas members were key regulators of carbon and nitrogen dynamics. In conclusion, the planting of E. angustifolia could improve the physical and chemical properties of the soil by releasing root exudates into the soil and increasing the diversity and richness of soil microbial communities to improve saline-alkali soil, providing a theoretical basis for improving saline-alkali soil and promoting the sustainable development of modern agriculture.

Short- and long-term effects of decabromodiphenyl ether (BDE-209) on sediment denitrification using a semi-continuous microcosm

The widespread use of decabromodiphenyl ether (BDE-209) resulted in its deposition in environmental media and biological matrices. However, to date, few studies focused on the effect of BDE-209 on microorganisms, and those available were investigated via an enclosed system completely cutting off the communication between testing system and its native environment. Herein, 4.0 mg/g BDE-209 acute exposure induced a 20% decline of NO_X-N (the sum of NO₃^--N and NO₂^--N) removal efficiency and a significant accumulation of NO₂^--N and N₂O. These inhibitory effects presented in a BDE-209 concentration-dependent manner. Using a semi-continuous microcosm, the inhibitory effects of BDE-209 on denitrification were observed to be significantly enhanced with the extending of exposure duration. Denitrifying genes assay illustrated that BDE-209 has an insignificant effect on the global abundance of denitrifying bacteria because of microbial exchange with its overlying water. But the utilization of electron donor (carbon substrate), the activity of electron transport system and denitrifying enzymes were significantly inhibited by BDE-209 exposure in a exposure-duration-dependent manner. Finally, insufficient electron donor and lower efficiency of electron transport and utilization on denitrifying enzymes deteriorated the denitrification performance. These results provided a new insight into BDE-209 influence on denitrification in the natural environment.

The Optical Characterization and Distribution of Dissolved Organic Matter in Water Regimes of Qilian Mountains Watershed

The constituents and content of dissolved organic matter (DOM) in the Qilian Mountain watershed were characterized with a spectroscopic technique, especially 3-DEEM fluorescence assisted by parallel factor (PARAFAC) analysis. The level of DOM in the surrounding area of Qinghai lake (thereafter the lake in this article specifically refers to Qinghai Lake)was highest at 9.45 mg C·L^-1 and about 3 times less (3.09 mg C·L^-1) in a cropland aquatic regime (the lowest value). In general, DOM was freshly autochthonously generated by plankton and plant debris, microorganisms and diagenetic effects in the aquatic environment (FI > 1.8). Component 1 (humic acid-like) and 3 (fulvic acid-like) determined the humification degree of chromophoric dissolved organic matter (CDOM). The spatial variation of sulfate and nitrate in the surrounding water regime of the lake revealed that organic molecules were mainly influenced by bacterial mediation. Mineral disintegration was an important and necessary process for fluorescent fraction formation in the cropland water regime. Exceptionally, organic moiety in the unused land area was affected by anespecially aridclimate in addition to microbial metabolic experience. Salinity became the critical factor determining the distribution of DOM, and the total normalized fluorescent intensity and CDOM level were lower in low-salinity circumstances (0.2-0.5 g·L^-1) with 32.06 QSU and 1.38 m^-1 in the grassland area, and higher salinity (0.6~0.8 g·L^-1) resulted in abnormally high fluorescence of 150.62 QSU and absorption of 7.83 m^-1 in the cropland water regime. Climatic conditions and microbial reactivity controlled by salinity were found to induce the above results. Our findings demonstrated that autochthonous inputs regulated DOM dynamics in the Qilian Mountains watershed of high altitude.

Effects of pollution load and salinity shock on nitrogen removal and bacterial community in two-stage vertical flow constructed wetlands

To understand the denitrification performance and microbial community of two-stage vertical flow constructed wetlands (TS-VFCWs) with iron ore/manganese ore and wood chips, COD and nitrogen removal were investigated under pollution load and salinity shock. High removal of COD (87%), NH₄⁺-N (97%), and NO₃^--N (98%) were achieved with increasing load, but the high pollutant load inhibited the denitrification performance in TS-VFCW with iron ore and wood chips. TS-VFCW with iron ore and wood chips showed good recovery potential with decreasing load. High NH₄⁺-N removal was observed in TS-VFCW with manganese ore and wood chips. Treatment with 3% salinity decreased COD and NH₄⁺-N removal but improved NO₃^--N removal, maintaining relatively good nitrogen removal. The addition of iron ore and manganese ore enriched nitrifying bacteria Flavobacterium and autotrophic denitrifying bacteria, while wood chips promoted heterotrophic denitrification and organic degradation. In addition, ubiquitous denitrifying bacteria under salinity ensured excellent denitrification performance.

Reductive soil disinfestation attenuates antibiotic resistance genes in greenhouse vegetable soils

Reductive soil disinfestation (RSD) is an emerging technique that ameliorates soil degradation, but its effects against antibiotic resistance genes (ARGs) were unclear. Here, we examined soil properties, ARG types and numbers, and ARG profiles, and bacterial community compositions following 4 soil treatments: control; straw addition (SA); water flooding (WF); and RSD, both straw addition and water flooding. The results showed that the numbers of ARG types and subtypes decreased by 10.8% and 21.1%, respectively, after RSD, and the numbers of ARGs decreased by 18.6%. The attenuated multidrug, beta-lactam, macrolide, and phenicol resistance genes in the RSD soil corresponded to a decreased relative abundance of ARG subtypes (i.e., adeF, mdtM, TypeB_NfxB, mecA, nalC, OXA-60, and cmlA4). Taxa in phyla Proteobacteria, Actinobacteria, and Deinococcus-Thermus were the main hosts for dominant ARG subtypes and were inhibited by RSD. The selected bacterial genera and soil properties explained 83.4% of the variance in ARG composition, suggesting that the improved soil properties and the reduced potential ARG hosts produced by the interactions of straw addition and water flooding are likely responsible for ARG attenuation by RSD. Therefore, RSD has the potential to mitigate ARG pollution in soils.