Shifts in soil microbial metabolic activities and community structures along a salinity gradient of irrigation water in a typical arid region of China

Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China

Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.

Comparative genomic analyses of aerobic planctomycetes isolated from the deep sea and the ocean surface

On the deep and dark seafloor, a cryptic and yet untapped microbial diversity flourishes around hydrothermal vent systems. This remote environment of difficult accessibility exhibits extreme conditions, including high pressure, steep temperature- and redox gradients, limited availability of oxygen and complete darkness. In this study, we analysed the genomes of three aerobic strains belonging to the phylum Planctomycetota that were isolated from two deep-sea iron- rich hydroxide deposits with low temperature diffusive vents. The vents are located in the Arctic and Pacific Ocean at a depth of 600 and 1,734 m below sea level, respectively. The isolated strains Pr1dT, K2D and TBK1r were analyzed with a focus on genome-encoded features that allow phenotypical adaptations to the low temperature iron-rich deep-sea environment. The comparison with genomes of closely related surface-inhabiting counterparts indicates that the deep-sea isolates do not differ significantly from members of the phylum Planctomycetota inhabiting other habitats, such as macroalgae biofilms and the ocean surface waters. Despite inhabiting extreme environments, our "deep and dark"-strains revealed a mostly non-extreme genome biology.

Variations in soil microbial communities in different saline soils under typical Populus spp. vegetation in alpine region of the Qaidam Basin, NW China

Salinization is a severe threat to agriculture and the environment in many areas, and the same in Qaidam Basin, Qinghai Province, Northwestern China. Microorganisms have an important influence on regulating the biochemical cycles of ecosystems; however, systematic research exploring microbial diversity and interactions with saline-soil ecosystems' environmental variables remains scarce. Thus, 16 S rRNA high-throughput sequencing was performed in this paper to characterize microbial diversity under different levels of salinized soils: non-salinized (NS, 2.25 g/L), moderately salinized (MS, 6.14 g/L) and highly salinized (HS, 9.82 g/L). The alpha diversity results showed that the HS soil was significantly different from the NS and MS soils. An analysis of similarity (ANOSIM) and a principal co-ordinates analysis (PCoA) indicated that NS and MS clustered closely while HS separated from the other two. Significant differences in microbial composition were observed at the taxonomic level. Proteobacteria (42.29-79.23 %) were the most abundant phyla in the studied soils. Gammaproteobacteria (52.49 and 66.61 %) had higher abundance in the MS and HS soils at the class level; Methylophaga and Pseudomonas were the predominant bacteria in the HS soil; and Azotobacter and Methylobacillus were abundant in the MS soil. Most genera belonging to Proteobacteria and Actinobacteria were detected via a linear discriminate analysis (LDA) effect size (LEfSe) analysis, which indicated that microbes with the ability to degrade organic matter and accomplish nutrient cycling can be well-adapted to salt conditions. Further analyses (redundancy analysis and Mantel test) showed that the microbial communities were mainly related to the soil salinity, electrical conductivity (EC1:5), total phosphorus (TP) and ammonia nitrogen (NH4+-N). Overall, the findings of the study can provide insights for better understanding the dominant indigenous microbes and their roles in biochemical cycles in different saline soils in the Qaidam Basin, Qinghai Province, China. The researches related to microbial community under typical poplar species should further clarify the mechanism of plant-microbial interaction and benefit for microbial utilization in salt soil remediation.

Salinity decreases the contribution of microbial necromass to soil organic carbon pool in arid regions

Saline soils are widely distributed in arid areas but there is a lack of mechanistic understanding on the effect of salinity on the formation and biochemical composition of soil organic carbon (SOC). We investigated the effects of salinity on the accumulation of microbial necromass under natural vegetation and in cropland in salt-affected arid areas stretching over a 1200-km transect in northwest China. Under both natural vegetation and cropland, microbial physiological activity (indicated by microbial biomass carbon normalized enzymatic activity) decreased sharply where the electrical conductivity approached 4 ds m-1 (a threshold to distinguish between saline and non-saline soils), but microbial biomass was only slightly affected by salinity. These indicated that a larger proportion of microbes could be inactive or dormant in saline soils. The contribution of fungal necromass C to SOC decreased but the contribution of bacterial necromass C to the SOC increased with increasing soil salinity. Adding fungal and bacterial necromass C together, the contribution of microbial necromass C to SOC in saline soils was 32-39 % smaller compared with non-saline soils. Fungal necromass C took up 85-86 % of microbial necromass C in non-saline soils but this proportion dropped to 60-66 % in saline soils. We suggested that the activity, growth, and turnover rate of microbes slowed by salinity was responsible for the decreased accumulation of fungal necromass in saline compared with non-saline soils, while the increased accumulation of bacterial residue in saline soils could be induced mainly by its slower decomposition. Soil microbial biomass was a poor predictor for the accumulation of microbial necromass in saline soils. We demonstrated a reduced contribution of microbial necromass to SOC and a shift in its composition towards the increase in bacterial origin in saline relative to non-saline soils. We concluded that salinity profoundly changes the biochemistry of SOC in arid regions.

Nitrogen-fixing cyanobacteria enhance microbial carbon utilization by modulating the microbial community composition in paddy soils of the Mollisols region

Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.

The Heterogeneous Habitat of Taiga Forests Changes the Soil Microbial Functional Diversity

The soil contains abundant and diverse microorganisms, which interrelate closely with the aboveground vegetation and impact the structure and function of the forest ecosystem. To explore the effect of vegetation diversity on soil microbial functional diversity in taiga forests, we selected significantly different important values of Larix gmelinii as experimental grouping treatments based on plant investigation from fixed plots in Da Xing'anling Mountains. Following that, we collected soil samples and applied the Biolog-ECO microplate method to investigate differences in carbon source utilization, features of functional diversity in soil microorganisms, and factors influencing them in taiga forests. The AWCD decreased as the important value of Larix gmelinii grew, and soil microorganisms preferred carboxylic acids, amino acids, and carbohydrates over polymers, phenolic acids, and amines. The Shannon and McIntosh indexes decreased significantly with the increase of the important value of Larix gmelinii (p < 0.05) and were positively correlated with soil SOC, MBC, C/N, and pH, but negatively with TN, AP, and AN. Redundancy analysis revealed significant effects on soil microbial functional diversity from soil C/N, SOC, AP, MBC, TN, pH, AN, and WC. To sum up, heterogeneous habitats of taiga forests with different important values altered soil microbial functional diversity.

Alleviation of cotton growth suppression caused by salinity through biochar is strongly linked to the microbial metabolic potential in saline-alkali soil

Biochar is a typical soil organic amendment; however, there is limited understanding of its impact on the metabolic characteristics of microorganisms in saline-alkaline soil microenvironment, as well as the advantages and disadvantages of plant-microorganism interactions. To elucidate the mechanisms underlying the impact of saline-alkali stress on cotton, a 6-month pot experiment was conducted, involving the sowing of cotton seedlings in saline-alkali soil. Three different biochar application levels were established: 0 % (C0), 1 % (C1), and 2 % (C2). Results indicated that biochar addition improved the biomass of cotton plants, especially under C2 treatment; the dry weight of cotton bolls were 8.15 times that of C0. Biochar application led to a rise in the accumulation of photosynthetic pigments by 8.30-51.89 % and carbohydrates by 7.4-10.7 times, respectively. Moreover, peroxidase (POD) activity, the content of glutathione (GSH), and ascorbic acid (ASA) were elevated by 23.97 %, 118.39 %, and 48.30 % under C2 treatment, respectively. Biochar caused a reduction in Na+ uptake by 8.21-39.47 %, relative electrical conductivity (REC) of plants, and improved K+/Na+ and Ca2+/Na+ ratio indicating that biochar alleviated salinity-caused growth reduction. Additionally, the application of biochar enhanced the absorption intensity of polysaccharide fingerprints in cotton leaves and roots. Two-factor co-occurrence analysis indicated that the key differential metabolites connected to several metabolic pathways were L-phenylalanine, piperidine, L-tryptophan, and allysine. Interestingly, biochar altered the metabolic characteristics of saline-alkali soil, especially related to the biosynthesis and metabolism of amino acids and purine metabolism. In conclusion, this study demonstrates that biochar may be advantageous in saline soil microenvironment; it has a favorable impact on how plants and soil microbial metabolism interact.

Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat

Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.

Endophyte inoculation enhanced microbial metabolic function in the rhizosphere benefiting cadmium phytoremediation by Phytolaccaacinosa

Microbial metabolic activities in rhizosphere soil play a critical role in plant nutrient utilization and metal availability. However, its specific characteristics and influence on endophyte assisted phytoremediation remains unclear. In this study, an endophyte strain Bacillus paramycoides (B. paramycoides) was inoculated in the rhizosphere of Phytolacca acinosa (P. acinosa), and microbial metabolic characteristics of rhizosphere soils were analyzed using Biolog system to investigate how they influence phytoremediation performance of different types of cadmium contaminated soil. The results indicated that endophyte B. paramycoides inoculation enhanced bioavailable Cd percentage by 9-32%, resulting in the increased Cd uptake (32-40%) by P. acinosa. With endophyte inoculation, the utilization of carbon sources was significantly promoted by 4-43% and the microbial metabolic functional diversity increased by 0.4-36.8%. Especially, B. paramycoides enhanced the utilization of recalcitrant substrates carboxyl acids, phenolic compounds and polymers by 48.3-225.6%, 42.4-65.8% and 15.6-25.1%, respectively. Further, the microbial metabolic activities were significant correlated with rhizosphere soil microecology properties and impact phytoremediation performance. This study provided new insight into the microbial processes during endophyte assisted phytoremediation.

River water influenced by shale gas wastewater discharge for paddy irrigation has limited effects on soil properties and microbial communities

The processes of hydraulic fracturing to extract shale gas generate a large amount of wastewater, and the potential impacts of wastewater discharge after treatment are concerning. In this field study, we investigated the effects of the irrigation of paddy fields for 2 consecutive years by river water that has been influenced by shale gas wastewater discharge on soil physicochemical properties, microbial community structure and function, and rice grain quality. The results showed that conductivity, chloride and sulfate ions in paddy soils downstream of the outfall showed an accumulative trend after two years of irrigation, but these changes occurred on a small scale (<500 m). Two-year irrigation did not cause the accumulation of trace metals (barium, cadmium, chromium, copper, lead, strontium, zinc, nickel, and uranium) in soil and rice grains. Among all soil parameters, the accumulation of chloride ions was the most pronounced, with concentrations in the paddy soil at the discharge site 13.3 times higher than at the upstream control site. The use of influenced river water for paddy irrigation positively increased the soil microbial diversity, but these changes occurred after two years of irrigation and did not occur after one year of irrigation. Overall, the use of river water affected by shale gas wastewater discharge for agricultural irrigation has limited effects on agroecosystems over a short period. Nevertheless, the possible negative effects of contaminant accumulation in soil and rice caused by longer-term irrigation should be seriously considered.

Metagenomic insights into the functional genes across transects in a typical estuarine marsh

Salt marshes are potentially one of the most efficient carbon (C) sinks worldwide and perform important ecosystem functions, but sea level rise alters marsh sediments properties and thus threatens microbial roles in ecosystem functioning. Yet, the mechanisms of interactions of biochemical processes with microorganisms and their functions are still not fully understood. Here, this study investigated metagenomic taxonomic and functional profiling from the water-land conjugation up to about 300 m, 1000 m, and 2500 m in three parallel transects, respectively, in Hangzhou Bay, China. The results showed that soil physicochemical factors drove metagenomic taxonomic and functional genes in the 2500-m transect significantly different from other sites. The 2500-m transect had a greater abundance of Chloroflexi and Acidobacteria but lower in Proteobacteria. The metagenomic functional genes related to Phosphorus Metabolism (PHO) and Potassium Metabolism (POT) increased in the 2500 m. Additionally, nutrient-cycling functions and the genera of Anaeromyxobacter, Roseiflexus, and Geobacter related to PHO, POT at 2500 m were significantly greater than those of other transects. Carbon cycling functions within Carbohydrates (CHO) also differed significantly across transects. These research results demonstrated that the relative abundance of metagenomic microorganisms and their functional genes were significantly separated across the three transects. The vegetation type, salinity, and soil properties might be among the influencing factors.

Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils

Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.

Saline-alkali stress reduces soil bacterial community diversity and soil enzyme activities

Saline-alkalisation of the soil environment and microorganism is a global challenge. However, relevant studies on the effects of saline-alkali stress on soil bacterial communities are limited. In this study, we investigated the effects of saline-alkali stress on the carbon source metabolic utilisation of the microbial community, bacterial diversity, and composition in soil using Biolog Ecoplate and 16S rRNA gene amplicon sequencing. Biolog Ecoplate results showed that saline-alkali stress decreased the metabolic activity and functional diversity, and changed the utilisation characteristics of carbon sources in soil microorganisms. Particularly, high level of saline-alkali stress significantly decreased the utilisation of carbohydrates and amino acids carbon sources. The results of 16S rRNA gene amplicon sequencing showed that high level of saline-alkali stress significantly reduced the diversity of soil bacterial communities. In addition, high level of saline-alkali stress significantly decreased the relative abundances of some key bacterial taxa, such as Gemmatimonas, Sphingomonas, and Bradyrhizobium. Furthermore, as saline-alkali content increased, the soil catalase, protease, urease, and sucrase activities also significantly decreased. Collectively, these results provide new insight for studies on the changes in the soil bacterial community and soil enzyme activity under saline-alkali stress.

Metagenomic analysis reveals antibiotic resistance genes and virulence factors in the saline-alkali soils from the Yellow River Delta, China

The propagation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in the saline-alkali soils and associated environmental factors remains unknown. In this study, soil samples from the Yellow River Delta, China with four salinity gradients were characterized by their physiochemical properties, and shotgun metagenomic sequencing was used to identify the ARGs and VFs carried by microorganisms. Soil salinization significantly reduced the relative abundances of Solirubrobacterales, Propionibacteriales, and Micrococcales, and quorum sensing in microorganisms. The number of ARGs and VFs significantly decreased in medium and high saline-alkali soils as compared with that in non-saline-alkali soil, however, the ARGs of Bacitracin, and the VFs of iron uptake system, adherence, and stress protein increased significantly in saline-alkali soils. Spearman analysis showed that the ARGs of fluoroquinolone, tetracycline, aminoglycoside, beta-lactam, and tigecycline were positively correlated with soil pH. Similarly, we observed an increased contribution to the ARGs and VFs by taxa belonging to Solirubrobacterales and Gemmatimonadales, respectively. The control plot was mainly improved from saline-alkali land through application of animal manure, which tended to contain large amounts of ARGs and VFs in this study. Further studies are needed to observe ARGs and VFs in the saline-alkali land for multiple years and speculate the potential risks caused by varied ARGs and VFs to the soil ecosystem and human health.

Soil salinity and its associated effects on soil microorganisms, greenhouse gas emissions, crop yield, biodiversity and desertification: A review

Significant research has been conducted on the effects of soil salinity issue on agricultural productivity. However, limited consideration has been given to its critical effects on soil biogeochemistry (e.g., soil microorganisms, soil organic carbon and greenhouse gas (GHG) emissions), land desertification, and biodiversity loss. This article is based on synthesis of information in 238 articles published between 1989 and 2022 on these effects of soil salinity. Principal findings are as follows: (1) salinity affects microbial community composition and soil enzyme activities due to changes in osmotic pressure and ion effects; (2) soil salinity reduces soil organic carbon (SOC) content and alters GHG emissions, which is a serious issue under intensifying agriculture and global warming scenarios; (3) soil salinity can reduce crop yield up to 58 %; (4) soil salinity, even at low levels, can cause profound alteration in soil biodiversity; (5) due to severe soil salinity, some soils are reaching critical desertification status; (6) innovate mitigation strategies of soil salinity need to be approached in a way that should support the United Nations Sustainable Development Goals (UN-SDGs). Knowledge gaps still exist mainly in the effects of salinity especially, responses of GHG emissions and biodiversity. Previous experiences quantifying soil salinity effects remained small-scale, and inappropriate research methods were sometimes applied for investigating soil salinity effects. Therefore, further studies are urgently required to improve our understanding on the effects of salinity, address salinity effects in larger-scale, and develop innovative research methods.

Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism

Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.

Influence of Bacillus subtilis strain Z-14 on microbial communities of wheat rhizospheric soil infested with Gaeumannomyces graminis var. tritici

Wheat take-all disease caused by Gaeumannomyces graminis var. tritici (Ggt) spreads rapidly and is highly destructive, causing severe reductions in wheat yield. Bacillus subtilis strain Z-14 that significantly controlled wheat take-all disease effectively colonized the roots of wheat seedlings. Z-14 increased the metabolic activity and carbon source utilization of rhizospheric microorganisms, thus elevating average well-color development (AWCD) values and functional diversity indexes of soil microbial communities. Z-14 increased the abundance of Bacillus in the rhizosphere, which was positively correlated with AWCD and functional diversity indexes. The Z-14-treated samples acquired more linkages and relative connections between bacterial communities according to co-occurrence network analyses. After the application of Ggt, the number of linkages between fungal communities increased but later decreased, whereas Z-14 increased such interactions. Whole-genome sequencing uncovered 113 functional genes related to Z-14’s colonization ability and 10 secondary metabolite gene clusters in the strain, of which nine substances have antimicrobial activity. This study clarifies how bacterial agents like Z-14 act against phytopathogenic fungi and lays a foundation for the effective application of biocontrol agents.

Role of plant growth-promoting rhizobacteria in boosting the phytoremediation of stressed soils: Opportunities, challenges, and prospects

Soil is considered as a vital natural resource equivalent to air and water which supports growth of the plants and provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably contamination/stress are the result of urbanisation, industrialization, and long-term use of synthetic fertiliser. Therefore, in the recent scenario, reclamation of contaminated/stressed soils has become a potential challenge. Several customized, such as, physical, chemical, and biological technologies have been deployed so far to restore contaminated land. Among them, microbial-assisted phytoremediation is considered as an economical and greener approach. In recent decades, soil microbes have successfully been used to improve plants' ability to tolerate biotic and abiotic stress and strengthen their phytoremediation capacity. Therefore, in this context, the current review work critically explored the microbial assisted phytoremediation mechanisms to restore different types of stressed soil. The role of plant growth-promoting rhizobacteria (PGPR) and their potential mechanisms that foster plants' growth and also enhance phytoremediation capacity are focussed. Finally, this review has emphasized on the application of advanced tools and techniques to effectively characterize potent soil microbial communities and their significance in boosting the phytoremediation process of stressed soils along with prospects for future research.

Irrigation water salinity structures the bacterial communities of date palm (Phoenix dactylifera)-associated bulk soil

The irrigation of date palms (Phoenix dactylifera) with saline groundwater is routinely practiced in the agroecosystems of arid environments because of freshwater scarcity. This leads to salts deposition in topsoil layers and increases soil salinization. However, how different irrigation sources affect soil microbiota is poorly understood. Bulk soil samples were collected from date farms receiving non-saline water and saline groundwater to examine bacterial communities using metabarcoding. Overall, bacterial diversity measures (Shannon diversity index, richness, and evenness) did not vary between irrigation sources. Bacterial communities were structured based on irrigation water sources and were significantly associated with their electrical conductivity. Of 5,155 operational taxonomic units (OTUs), 21.3% were unique to soil irrigated with saline groundwater, 31.5% received non-saline water irrigation, and 47.2% were shared. The Proteobacteria abundance was higher in soil under saline groundwater irrigation while Actinobacteriota abundance was lower. A compositional shift at the genera level was also evident; the abundance of Subgroup_10 and Mycobacterium was higher under saline groundwater irrigation. Mycobacterium was a key indicator of OTU under saline groundwater irrigation while Solirubrobacter was an indicator of non-saline water irrigation. Functional gene analyses showed enrichment of fatty acid, cell wall, and starch biosynthesis pathways in soil under saline groundwater irrigation. These findings provide insights into how "salinity filtering" influences bacterial communities, key taxa, and the potential metabolic function in soil under increasing irrigation water salinities, and have broad implications for arid agroecosystems.

Insight into halotolerance of a robust heterotrophic nitrifying and aerobic denitrifying bacterium Halomonas salifodinae

Studies toward biotreating hypersaline wastewater containing different salts and halotolerant mechanism of robust strains are important but still rare. Here an isolated bacterium Halomonas salifodinae can perform simultaneous nitrification and denitrification (SND) at 15% salinity, showing high nitrogen removal efficiencies of over 98% via response surface methodology optimization. Besides NaCl, this robust strain had high resistance to other salts (KCl, Na₂SO₄, and K₂SO₄) and can efficiently remove nitrogen in saline wastewater containing heavy metals such as Fe(II), Mn(II), Zn(II), Cr(VI), Ni(II), and Cu(II). After repeated-batch culturing at different salinities, the treated strains with different halotolerant capabilities were used as single strain model to study halotolerant mechanism via metabolic analysis. The halotolerant bacterium can convert D-proline and glutamic acid to glutamine as well as lactulose to trehalose. The accumulated intracellular compatible solutes can resist high osmotic pressure and bound water molecule in hypersaline wastewater to accomplish high-efficiency SND processes.

Simultaneous nitrification and denitrification of hypersaline wastewater by a robust bacterium Halomonas salifodinae from a repeated-batch acclimation

Biotreatment of hypersaline wastewater requires robust strains with high resistance to activity inhibition and even bacterium death, which remains a worldwide challenge. Here Halomonas salifodinae, a simultaneous nitrification and denitrification (SND) bacterium, was isolated by performing repeated-batch acclimation, showing efficient nitrogen removal at 0-15% salinity and low activity inhibition prominently superior to that of other strains such as Pseudomonas sp. and Acinetobacter sp. Community analysis as well as comparison of microbial activity at different salinities revealed an increased relative abundance of halotolerant populations by stimulating their salt tolerance during the repeated-batch process. For single or mixed nitrogen sources at 15% salinity, the SND efficiencies of the isolated strain reached above 95%. The high activities were attributed to the key enzymes AMO and HAO for nitrification as well as NAP and NIR for denitrification. The findings provide a promising acclimation pathway to obtain robust bacteria for biotreatment of hypersaline wastewater.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

Soil salinity regulation of soil microbial carbon metabolic function in the Yellow River Delta, China

The ecological consequences of soil salinization, one of the major causes of soil degradation worldwide, on soil carbon (C) emissions are well known, but less is known about the related microbial C metabolic function. We conducted laboratory incubation experiments on soil samples under a salt gradient at four levels (non-saline, low, medium, and high salinity soils) from coastal saline-alkaline soil of the Yellow River Delta, China, to assess the role of soil salinity in regulating C emissions and microbial abundance. We also evaluated the associations between salt content and the read number of microbial C metabolism genes by determining the soil metagenomes. We found that soil salinity was negatively related to soil C, nitrogen (N) content, C emissions, bacterial gene copy number, and the relative abundances of Actinobacteria, Thermoleophilia, and Betaproteobacteria, but positively related to the C/N ratio and the relative abundance of Gemaproteobacteria and Halobacteria. Increases in soil salinity correlated with decreases in carbohydrate metabolism and gene abundances of glycosyl transferases and glycoside hydrolases based on the metagenomic data. In contrast, the enzyme active genes of carbohydrate esterases and auxiliary activities were positively related to soil salinity. This study provides a clear understanding of the response of soil microbial communities and their C metabolic functions to soil salinity. We offer evidence that soil salinity has significant effects on microbial communities and soil C metabolic functions, resulting in an overall negative effect on soil C emissions.

Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO₄ ^2-, SOC, HCO₃ ^-, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

Unraveling bacterial community structure and function and their links with natural salinity gradient in the Yellow River Delta

Salinization can change the soil environment and affect microbial processes. In this study, soil samples were collected from Zone A (Phragmites australis wetlands), Zone B (P. australis and Suaeda salsa wetlands), and Zone C (Spartina alterniflora wetlands) in the Yellow River Delta. The microbial community and functional potential along the natural salinity gradient were investigated. Total nitrogen, ammonia nitrogen, and soil organic matter presented a downward trend, and salinity first increased and then decreased from Zone A to Zone C. Nitrospira and norank_f_Nitrosomonadaceae were widely distributed throughout the zones. Denitrifying bacteria Alcanivorax, Marinobacterter, and Marinobacterium were abundant in Zone B and preferred high salinity levels. However, denitrifying bacteria Azoarcus, Flavobacterium, and Pseudomonas were mainly distributed in low-salinity Zones A and C, suggesting their high sensitivity to salinity. Dissimilatory nitrate reduction to ammonia (DNRA) bacteria Aeromonas and Geobacter dominated Zone C, whereas Caldithrix performed DNRA in Zone B. Interestingly, DNRA with organic matter as the electron donor (C-DNRA) occurred in Zone A; DNRA coupled with sulfide oxidation (S-DNRA) was dominant in Zone B; and C-DNRA and DNRA with divalent iron as electron donor and S-DNRA occurred simultaneously in Zone C. Salinity was the key factor distinguishing low and high salinity zones, and total nitrogen and total phosphorus had important effects at the phylum and genus levels. The abundance of genes encoding cell growth and death was relatively stable, indicating that the microbial community had good environmental adaptability. The genes related to the biodegradation of xenobiotics and the metabolism of terpenoids and polyketides were abundant in Zone B, revealing high metabolic potential for exogenous refractory substances. The microorganisms under low-salinity Zones A and C were more sensitive to environmental changes than those under Zone B. These results suggest that salinity plays important roles in microbial processes and shapes specific functional zones in coastal wetlands.

Urbanization pressures alter tree rhizosphere microbiomes

The soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban-rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural-urban gradient indicate pH, Ca⁺, and organic matter are largely responsible for driving relative abundance of specific SMC members.

Bacterial community variations with salinity in the saltwater-intruded estuarine aquifer

Bacterial community has been significantly enrolled in the biogeochemical cycling of the coastal subsurface ecosystem. The bacterial community variations with salinity have been extensively investigated in the surface environment, such as lake, soil, and estuary, but not in the subsurface environment. Here we explore the responses of bacterial populations to the salinity and other environmental factors (EFs) by considering both the abundant and rare sub-community in a coastal Holocene groundwater system. Our study results indicate that the bacterial diversity was independent of the salinity in both the abundance and rare sub-community. Besides diversity, no flourishing of abundant bacteria relative abundance is observed with increasing or decreasing salinity. Yet the rare taxa exhibit a bio-growth with salinity, which has a significant correlation (p < 0.001) with sulfate concentration. The responses of the abundant sub-community taxa to nutrients, temperature, pH, and dissolved oxygen are insensitive. However, the correlation between δ¹⁸O, δD and the entire community diversity is significant, which demonstrates the bacterial community is affected by the groundwater origin. Besides, not all the species in one class or order are necessarily shaped by the same factor. To quantify the impact of EFs on the community properties, analyses in different taxonomic levels is suggested. These findings imply that the spatial organization of microbial communities is complicated and influenced by multiple factors on a regional scale. The investigated results are useful for understanding biogeochemical processes in the coastal groundwater.

Temperature and salinity drive comammox community composition in mangrove ecosystems across southeastern China

Complete ammonia-oxidizing (comammox) microorganisms are newly recognized nitrifying bacteria found in natural and engineered ecosystems. Mangrove ecosystems are hotspots for nitrogen cycling, but the knowledge of comammox diversity and abundance, and particularly, driving factors, in these ecosystems is scarce. We here used deep sequencing to investigate comammox diversity in six mangrove ecosystems across southeastern China. Our results showed that comammox microorganisms in mangrove sediments were extremely diverse. Phylogenetic analysis revealed a novel comammox group within clade A that formed a distinct cluster for which no reference sequence existed, implying their potential uniqueness. Quantitative PCR demonstrated that comammox abundance was slightly higher than that of the canonical ammonia-oxidizing bacteria but significantly lower than that of ammonia-oxidizing archaea, indicating they are not the dominant ammonia oxidizers in mangrove ecosystems. Finally, variation partition analysis revealed a significant decrease in similarity of comammox communities along the geographical distance, and a pronounced effect of the geographic factors and sediment attributes on the composition of comammox microorganisms and the abundance variations of ammonia oxidizers. Temperature and salinity were the most important contributing factors that shaped the comammox community. Further, detection of diverse comammox microorganisms in extremely high-salinity sediments suggested that this community could adapt to high salinity environments, which indicates salinity may not be a critical factor resulting in the absence of comammox microorganisms in open-ocean environments. This study expanded the current understanding of the diversity and niche preference of comammox in mangrove ecosystems, and further enhanced our understanding of adaptation potential of comammox communities.

Effects of pyrolysis temperature on soil-plant-microbe responses to Solidago canadensis L.-derived biochar in coastal saline-alkali soil

Because salinity of coastal soils is drastically increasing, the application of biochars to saline-alkali soil amendments has attracted considerable attention. Various Solidago-canadensis-L.-derived biochars prepared through pyrolysis from 400 to 600 °C were applied to coastal saline-alkali soil samples to optimise the biochar pyrolysis temperature and investigate its actual ecological responses. All biochars reduced the soil bulk density and exchangeable sodium stress and increased soil water-holding capacity, cation exchange capacity, and organic matter content. Principal-component-analysis results showed that pyrolysis temperature played an important role in the potential application of biochars to improve the coastal saline-alkali soil, mainly contributed to ameliorating exchangeable sodium stress and decreasing biochar-soluble toxic compounds. Furthermore, soil bulk density and organic matter, as well as carboxylic acids, phenolic acids and amines of biochar were major driving factors for bacterial community composition. Compared to low-temperature biochar (pyrolyzed below 550 °C), which showed higher toxicity for Brassica chinensis L. growth due to the higher content of carboxylic acids, phenols and amines, high-temperature biochar (pyrolyzed at or above 550 °C) possessed less amounts of these toxic functional groups, more beneficial soil bacteria and healthier for plant growth. Therefore, high-temperature biochar could be applied as an effective soil amendment to ameliorate the coastal saline-alkali soil with acceptable environmental risk.

Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai-Tibetan Lakes

Uncovering microbial response to salinization or desalinization is of great importance to understanding of the influence of global climate change on lacustrine microbial ecology. In this study, to simulate salinization and desalinization, sediments from Erhai Lake (salinity 0.3-0.8 g/L) and Chaka Lake (salinity 299.3-350.7 g/L) on the Qinghai-Tibetan Plateau were transplanted into different lakes with a range of salinity of 0.3-299.3 g/L, followed by in situ incubation for 50 days and subsequent geochemical and microbial analyses. Desalinization was faster than salinization in the transplanted sediments. The salinity of the transplanted sediment increased and decreased in the salinization and desalinization simulation experiments, respectively. The TOC contents of the transplanted sediments were lower than that of their undisturbed counterparts in the salinization experiments, whereas they had a strong negative linear relationship with salinity in the desalinization experiments. Microbial diversity decreased in response to salinization and desalinization, and microbial community dissimilarity significantly (P < 0.01) increased with salinity differences between the transplanted sediments and their undisturbed counterparts. Microbial groups belonging to Gammaproteobacteria and Actinobacteria became abundant in salinization whereas Bacteroidetes and Chloroflexi became dominant in desalinization. Among the predicted microbial functions, hydrogenotrophic methanogenesis, methanogenesis through CO₂ reduction with H₂, nitrate/nitrogen respiration, and nitrification increased in salinization; in desalinization, enhancement was observed for respiration of sulfur compounds, sulfate respiration, sulfur respiration, thiosulfate respiration, hydrocarbon degradation, chemoheterotrophy, and fermentation, whereas depressing was found for aerobic ammonia oxidation, nitrate/nitrogen respiration, nitrification, nitrite respiration, manganese oxidation, aerobic chemoheterotrophy, and phototrophy. Such microbial variations could be explained by changes of transplantation, salinity, and covarying variables. In summary, salinization and desalinization had profound influence on the geochemistry, microbial community, and function in lakes.

Isolation and characterization of a salt-tolerant denitrifying bacterium Alishewanella sp. F2 from seawall muddy water

A salt-tolerant denitrifying bacterium strain F2 was isolated from seawall muddy water in Dalian City, Liaoning Province, China. Strain F2 was identified by morphological observations, physiological and biochemical characteristics and 16 S rDNA identification. The salt tolerance of strain F2 was verified and the factors affecting the removal ability of strain F2 to nitrous nitrogen (NO2-N) and nitrate nitrogen (NO3-N) in saline conditions were investigated. Strain F2 was identified as Alishewanella sp., named Alishewanella sp. F2. Strain F2 can tolerate NaCl concentrations up to 70 g/L, and its most efficient denitrification capacity was observed at NaCl concentrations of 0-30 g/L. In the medium with NaCl concentrations of 0-30 g/L, strain F2 exhibited high removal efficiencies of NO2-N and NO3-N, with the removal percentages for both NO2-N and NO3-N of approximately 99%. In saline conditions with 30 g/L NaCl, the optimum culture pH, NaNO2 initial concentrations and inoculation sizes of strain F2 were 8-10, 0.4-0.8 g/L and 5-7%, respectively. Strain F2 was highly effective in removing NO2-N and NO3-N in saline conditions, and it has a good application potential in saline wastewater treatment.

Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

Comparative effects of the recovery from sulfuric and nitric acid rain on the soil enzyme activities and metabolic functions of soil microbial communities

Acid rain (AR) is a serious issue in China, particularly in the Yangtze River Delta region where the economy has undergone rapid development. Over the last few years, the composition of acid rain in the Yangtze River Delta region has gradually changed from sulfuric acid rain (SAR) to nitric acid rain (NAR) due to controls on SO₂ emissions, but increased NO_x emissions. These changes have made ecosystems more complex. For this study, we halted AR treatments in Quercus acutissima forest plots that had received simulated AR for one year and monitored them from the following February to November. We investigated their soil resident enzyme and microbial metabolic activities, as well as community functional diversity. The results revealed that AR treatments negatively affected both the soil microbial activity and soil microbial community functional diversity; however, both managed to recover over time, once the AR treatments were stopped. During the AR treatment and recovery periods, four main categories (carbohydrates, carboxylic acids, amino acids, and polymers) were dominantly utilized. The utilization of pyruvic acid, which was affected by the AR treatments, as well as d-mannitol and tween 80, accounted for changes in the peak values of the C substrate groups during the AR treatment recovery period. Finally, changes in the activities of soil enzymes recorded following AR recovery, were closely related to the utilization of six C substrate groups. Our results suggested that the recovery of soils following the cessation of NAR stress was more rapid than from SAR. Further, that short-term NAR could be easily treated during the transformation from SAR to NAR in the Yangtze River Delta region. These results might also enrich the basic data relating to post-AR treatments on the soil environment, while having significance toward guiding further studies on the recovery of ecosystems from AR.

Long-term cover cropping seasonally affects soil microbial carbon metabolism in an apple orchard

Groundcover management can significantly affect soil microbial metabolic activities, especially carbon metabolism, in apple orchards. However, there have been few studies on the effects of groundcover on the seasonality of soil microbial carbon metabolism. We, therefore, studied soil microbial carbon metabolism in an apple orchard on China's Loess Plateau under four single species cover crops (the grass Dactylis glomerata L., and the legumes Trifolium repens, Coronilla varia L., Lotus corniculatus L.) during spring, summer and fall. Cover cropping significantly, but differentially, promoted soil microbial carbon metabolism in spring and fall. However, cover cropping leads to a significant reduction of soil moisture in spring and summer due to the competition of soil moisture between the cover crops and apple trees, which probably lead to the changes in types of carbon substances metabolizing by soil microbes in summer. Besides, cover crop significantly enhanced soil organic carbon contents between three seasons while clean cultivation had slight, non-significant effects. The promotion of soil microbial metabolic activities was probably an important mechanism for the carbon accumulation, and we postulate that leguminous cover plants may have significantly different effects, mediated through their root exudates, from grasses on soil carbon contents.

Antibiotic resistance genes attenuated with salt accumulation in saline soil

Salt accumulation on the surface of the soil layer driven by the strong evaporation is a natural phenomenon that usually happens in the dry season, particularly on the coastal lands reclaimed from tidal flats. However, the influence of salt accumulation on the distribution profile of antibiotic resistance genes (ARGs) and mobile gene elements (MGEs) remains unclear. In this study, we sampled a wild saline soil where the salt accumulation was frequently observed to investigate the vertical distribution profiles of ARGs and MGEs. The results showed that an increasing gradient of ARGs and MGEs was observed from the top to deep layer with the decreasing of electrical conductivity (EC1:5 values) indicating the salt-influenced attenuation of ARGs in the saline soil. The competing test suggested that the attenuation of ARGs in response to salinity gradient was attributable to the elimination of the ARG-harboring plasmids, due to the reduction of the relative fitness of plasmid-harboring strains. Additionally, the network analyses showed that the attenuation of ARGs might be associated with decreased abundance of Actinobacteria. Overall, this study identifies that salinity as an abiotic stress could re-shape the distribution of ARGs, which may influence the dissemination of ARGs in the environment.

The structure of denitrifying microbial communities in constructed mangrove wetlands in response to fluctuating salinities

In this study, the experimental vertical-flow constructed wetland (CW) systems planted with the salt-tolerant mangrove species Kandelia candel were established to investigate the influence of salinity fluctuations on the denitrification performance and denitrifying microbial community structure of the CWs. The high-throughput sequencing analysis showed that 10-13 genera aerobic microbes had been enriched in the upper layer of wetland matrix in the depth of 10-25 cm, with the relative abundance accounting for 19.1 ± 7.9%. Although the ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were inhibited significantly in the CW systems with salinity levels in the range of 0.9-1.8%, the aerobic denitrifying (AD) bacteria including Pseudomonas, Acinetobacter and Aeromonas, removed 99% of ammonia nitrogen from the influent by heterotrophic nitrification (HN) functions, and conducted denitrification at the same time to remove 90% of the TN in the system, indicating that the wetland test system successfully enriched a variety of aerobic denitrifying bacterial communities under different salinity conditions. Not only the nitrogen removal efficiency but also the adaptability of the wetland system to salinity fluctuations had been improved by the enriched HN-AD bacteria. In addition, HN-AD bacterial communities can conduct both nitrification and denitrification in the middle and upper layers of the vertical flow wetland, hereby saving the reaction space of the constructed wetland and reducing the construction cost.

Soil aggregate-associated bacterial metabolic activity and community structure in different aged tea plantations

Revealing the dynamics of soil aggregate-associated microbial (particularly bacterial) metabolic activity and community structure is of great importance to maintain the soil health and microbial community stability in tea plantation ecosystems. In this study, the bacterial metabolic activity (as measured by Biolog Eco MicroPlates) and community structure (as measured by high-throughput sequencing) were analyzed in soil aggregates, which were collected at the 0-20 cm depth in four tea plantations with different ages (16, 23, 31, and 53 yrs.) in the areas of Western Sichuan, China. A dry-sieving procedure was adopted to separate soil aggregates into four fractions, including >2, 2-1, 1-0.25, and <0.25 mm. In all the tea plantations, the highest levels of soil bacterial metabolic activity (as indicated by average well color development, AWCD) and community diversity (as indicated by Chao 1 and Shannon indices) appeared in the >2 mm fractions, which indicated that these aggregate fractions with complex bacterial communities not only provided biological buffering, but also prevented the dominance of individual microorganisms through predation or competition. Soil aggregates with >2 mm were concentrated in the 23 yrs. tea plantation, implying that this tea plantation possessed the relatively suitable soil environments to the growth and proliferation of soil bacteria, thus increasing their metabolic activity and community diversity. After 23 yrs. of tea planting, the reduction of the >2 mm fractions in the whole-soil accounted for the degradation of soil bacterial communities to some extent. In the meanwhile, soil microbial quotient (the ratio of soil microbial biomass C to organic C) and pH were also important drivers of the variations in soil bacterial communities during tea planting. This study underscored the requirement for sustainable soil managements which could maintain the soil health and bacterial community stability after 23 yrs. of tea planting in the areas of Western Sichuan, China.

Microbial aerobic denitrification dominates nitrogen losses from reservoir ecosystem in the spring of Zhoucun reservoir

The mechanism and factors influencing nitrogen loss in the Zhoucun reservoir were explored during the spring. The results showed that the nitrate and total nitrogen concentration decreased from 1.84 ± 0.01 mg/L and 2.34 ± 0.06 mg/L to 0.06 ± 0.01 mg/L and 0.48 ± 0.09 mg/L, respectively. Meanwhile, the nitrate and total nitrogen removal rate reached 97.02% ± 0.25 and 79.38% ± 3.32, respectively. Moreover, the abundance of nirS gene and aerobic denitrification bacteria increased from 1.04-3.38 × 10³ copies/mL and 0.71 ± 0.22 × 10² cfu/mL to 5.36-5.81 × 10³ copies/mL and 8.64 ± 2.08 × 10³ cfu/mL, respectively. The low MW fractions of DOM (<5 kDa) increased from 0.94 ± 0.02 mg/L in February to 1.51 ± 0.09 mg/L in April. E3/E4 and absorption spectral slope ratio (S_R) showed that fulvic acid accounted for the main proportion with autochthonous characteristics. These findings were consistent with the fluorescence components and fluorescence characteristic indices based on EEM-PARAFAC. Meanwhile, the microbial metabolism activity increased significantly from February to April, which contributed to the cycle of nutrients within the reservoir water system. Moreover, the abundance of the bacterial species involved in denitrification (Exiguobacterium, Brevundimonas, Deinococcus, Paracoccus, and Pseudomonas) increased significantly. The relative abundance of KOs related to nitrogen metabolism, were initially increased and then decreased. Specifically, K02567 (napA) represented the main proportion of KOs related to denitrification. The abundance of napA-type denitrifying bacteria (Dechloromonas, Pseudomonas, Azospira, Rhodopseudomonas, Aeromonas, Zobellella, Sulfuritalea, Bradyrhizobium, Achromobacter, Enterobacter, Thauera, and Magnetospirillum) increased significantly during the period of nitrogen loss. Furthermore, the levels of nitrate, T, DO, and AWCD were the most important factors affecting the N-functional bacteria composition. The systematic investigation of the nitrogen loss would provide a theoretical foundation for the remediation of the water reservoir via aerobic denitrification in the future.

Coal chemical reverse osmosis concentrate treatment by membrane-aerated biofilm reactor system

Coal chemical reverse osmosis concentrate (ROC), which is characterized by high salinity and high organics, remains as a serious environmental problem. In this study, a lab-scale three-stage membrane-aerated biofilm reactor (MABR) system was designed to treat such a ROC. The effects of influent salinity and operating parameters (pH, DO and HRT) on the treatment efficiency were discussed. The removal efficiencies of COD, NH₄-N and TN under the optimal operating parameters reached to 81.01%, 92.31% and 70.72%, respectively. Simultaneous nitrification and denitrification (SND) as well as shortcut nitrogen removal were achieved. The salinity less than 3% did not induce significant decrease in treatment efficiency and microbial communities. Moreover, the dominant phyla in biofilms were Proteobacteria and Bacteroidetes. This work demonstrated MABR had great potential in ROC treatment.

Salinity is a key factor driving the nitrogen cycling in the mangrove sediment

Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres.

Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium

With the close relationship between saline environments and industry, polycyclic aromatic hydrocarbons (PAHs) accumulate in saline/hypersaline environments. Therefore, PAHs degradation by halotolerant/halophilic bacteria has received increasing attention. In this study, the metabolic pathway of phenanthrene degradation by halophilic consortium CY-1 was first studied which showed a single upstream pathway initiated by dioxygenation at the C1 and C2 positions, and at several downstream pathways, including the catechol pathway, gentisic acid pathway and protocatechuic acid pathway. The effects of salinity on the community structure and expression of catabolic genes were further studied by a combination of high-throughput sequencing, catabolic gene clone library and real-time PCR. Pure cultures were also isolated from consortium CY-1 to investigate the contribution made by different microbes in the PAH-degrading process. Marinobacter is the dominant genus that contributed to the upstream degradation of phenanthrene especially in high salt content. Genus Halomonas made a great contribution in transforming intermediates in the subsequent degradation of catechol by using catechol 1,2-dioxygenase (C12O). Other microbes were predicted to be mediating bacteria that were able to utilize intermediates via different downstream pathways. Salinity was investigated to have negative effects on both microbial diversity and activity of consortium CY-1 and consortium CY-1 was found with a high degree of functional redundancy in saline environments.

Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing

Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student’s t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student’s t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance.