Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system

Hypoxia exerts greater impacts on shallow groundwater nitrogen cycling than seawater mixture in coastal zone

There is no doubt that hypoxia and seawater mixture are profoundly affecting the global nitrogen (N) cycle. However, their mechanisms for altering N cycling patterns in shallow coastal groundwater are largely unknown. Here, we examined shallow groundwater N transformation characteristics (dissolved inorganic N and related chemical properties) in the coastal area of east and west Shenzhen City. Results showed that common hypoxic conditions exist in this study area. Ions/Cl- ratios indicated varying levels of saltwater mixture and sulfide formation across this study area. Dissolved oxygen (DO) affects the N cycle process by controlling the conditions of nitrification and the formation of sulfides. Salinity affects nitrification and denitrification processes by physiological effects, while sulfide impacts nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) processes through its own toxicity mechanism and the provision of electron donors for DNRA organisms. Redundancy analysis (RDA) results indicate that the influence magnitude is in the following order: DO > sulfide > salinity. Seawater mixture weakened the nitrification and denitrification of groundwater by changing salinity, while hypoxia and its controlled sulfide formation not only weaken nitrification and denitrification but also stimulated the DNRA process and promotes N regeneration. In this study area, hypoxia is considered to exert greater impacts on N cycling in the coastal shallow groundwater than seawater mixture. These findings greatly improve our understanding of the consequences of hypoxia and seawater mixture on coastal groundwater N cycling.

Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.

High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay

Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.

Geochemical factors impacting nitrifying communities in sandy sediments

Sandy sediment beaches covering 70% of non-ice-covered coastlines are important ecosystems for nutrient cycling along the land-ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p-value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification of amoA genes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater-derived nutrients to coastal waters.

Who does better for in-situ eutrophic remediation in anoxic environment improvement and nutrient removal: MgO2 versus CaO2

The long-term insufficient dissolved oxygen (DO), excessive nitrogen (N) and phosphorus (P) have become the main causes of the troublesome eutrophication. Herein, a 20-day sediment core incubation experiment was conducted to comprehensively evaluate the effects of two metal-based peroxides (MgO₂ and CaO₂) on eutrophic remediation. Results indicated that CaO₂ addition could increase DO and ORP of the overlying water more effectively and improve the anoxic environment of the aquatic ecosystems. However, the addition of MgO₂ had a less impact on pH of the water body. Furthermore, the addition of MgO₂ and CaO₂ removed 90.31% and 93.87% of continuous external P in the overlying water respectively, while the removal of NH₄⁺ was 64.86% and 45.89%, and the removal of TN was 43.08% and 19.16%. The reason why the capacity on NH₄⁺ removal of MgO₂ was higher than that of CaO₂ is mainly that PO₄^3- and NH₄⁺ can be removed as struvite by MgO₂. Compared with MgO₂, mobile P of the sediment in CaO₂ addition group was reduced obviously and converted to more stable P. Notably, the microbial community structure of sediments was optimized by MgO₂ and CaO₂, which showed that the relative abundance of anaerobic bacteria decreased and that of aerobic bacteria increased significantly, especially some functional bacteria involved in the nutrient cycle. Taken together, MgO₂ and CaO₂ have a promising application prospect in the field of in-situ eutrophication management.

Salinity significantly reduces plastic-degrading bacteria from rivers to oceans

Microplastics (MPs) are found in rivers and offshore areas. However, there is a lack of detailed research on the changes of surface microbial species attached to MPs when MPs enter the sea. Moreover, no study has been conducted on changes to plastic-degrading bacteria during this process. In this study, using rivers and offshore in Macau, China as examples, bacterial diversity and bacterial species composition attached to surface water and MPs at four river sampling stations and four offshore sampling stations around Macau were studied. Plastic-degrading bacteria, plastic-related metabolic processes, and plastic-related enzymes were analyzed. The results showed that MPs-attached bacteria in rivers and offshore were different with the planktonic bacteria (PB). The proportion of major families on the surface of MPs continued to increase from rivers to estuaries. MPs could significantly enrich plastic-degrading bacteria both in rivers and offshore. The proportion of plastic-related metabolic pathways on the surface bacteria of MPs in rivers was higher than that in offshore waters. Bacteria on the surface of MPs in rivers may induce higher plastic degradation than offshore. Salinity significantly alters the distribution of plastic-degrading bacteria. MPs may degrade more slowly in the oceans, posing a long-term threat to marine life and human health.

Effects of tidal action on the stability of microbiota, antibiotic resistance genes, and microplastics in the Pearl River Estuary, Guangzhou, China

In this study, the 16S rRNA gene amplicon sequencing technique was used to explore the microbial diversity and differences in the water environment of the Pearl River Estuary in Nansha District with various land use types such as the aquaculture area, industrial area, tourist area, agricultural plantation, and residential area. At the same time, the quantity, type, abundance, and distribution of two types of emerging environmental pollutants, antibiotic resistance genes (ARGs) and microplastics (MPs), are explored in the water samples from different functional areas. The results show that the dominant phyla in the five functional regions are Proteobacteria, Actinobacteria and Bacteroidetes, and the dominant genera are Hydrogenophaga, Synechococcus, Limnohabitans and Polynucleobacter. A total of 248 ARG subtypes were detected in the five regions, belonging to nine classes of ARGs (Aminoglycoside, Beta_Lactamase, Chlor, MGEs, MLSB, Multidrug, Sul, Tet, Van). Blue and white were the dominant MP colors in the five regions; 0.5-2 mm was the dominant MP size, and cellulose, rayon, and polyester comprised the highest proportion of the plastic polymers. This study provides the basis for understanding the environmental microbial distribution in estuaries and the prevention of environmental health risks from ARGs and microplastics.

Soil acidification induced variation of nitrifiers and denitrifiers modulates N2O emissions in paddy fields

Soil acidification is a major land degradation process globally, and impacts soil nitrogen (N) transformation. However, it is still not well known how soil acidification affects net N mineralization and nitrification, especially N-cycling microbes and nitrous oxide (N₂O) emissions. Hence, three soils characterized by different soil pH values (5.5, 6.3, and 7.7) were collected from the paddy fields, and experiments were conducted to evaluate the effect of soil acidification on net N mineralization and nitrification, and N₂O emissions. Compared to those in the soils with pH 7.7 and 6.3, net N mineralization, net nitrification, and N₂O emissions were decreased by 75-76 %, 89-91 %, and 19-48 %, respectively, in the soil with pH 5.5, while net N nitrification and N₂O emissions decreased by 18 % in the soil with pH 6.3 when compared to those in the soil with pH 7.7. The significantly decreased net nitrification in the soils with pH 6.3 and 5.5 was mainly attributed to the limited N availability and abundance of nitrification-related microbes including ammonia-oxidizing bacteria and complete ammonia-oxidizers. The decrease in N₂O emissions of soils with pH 6.3 and 5.5 had mainly resulted from decreasing nitrification and denitrification via suppressing microbes including nirS and fungal nirK and limiting N availability. Hence, this study provides new insights and improves our understanding of how soil acidification regulates N mineralization, nitrification, and N₂O emissions in paddy soils, which gives guidance on developing N management strategies for sustainable production and N₂O mitigation in acid soils.

Seawater intrusion alters nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions: Based on Bayesian isotope mixing model and microbial functional network

Seawater intrusion is a global coastal environmental issue of great concern and significantly impacts the regional biogeochemical environment and material cycles, including nitrogen cycling. To reveal the mechanism of seawater intrusion altering nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions, the Bayesian mixing model (δ¹⁵N-NO₃^- and δ¹⁸O-NO₃^-) and 16S rDNA gene amplicon sequencing are used to establish nitrogen cycling pathways and microbial functional network. The results show that the nitrate in the coastal groundwater is from manure and septic waste (M&S, over 44 %), soil organic nitrogen (SON, over 20 %), and nitrogen fertilizer (FN, over 16 %). The hydrological interaction has promoted the coupling between material cycling and microbial community in the coastal groundwater systems. Among them, precipitation infiltration has caused the gradual decrease of specific microbes along the flow direction, such as Lactobacillus, Acinetobacter, Bifidobacterium, etc. And seawater intrusion has caused the mutations of specific microbes (Planktomarina, Clade_Ia, Wenyingzhuangia, Glaciecola, etc.) and convergence of microbial community at the salt-freshwater interface in the aquifer. In the coastal intruded aquifer systems, the nitrogen cycling pattern can be divided into oxidation and reduction processes. The oxidation process involves the enhancement of nitrification while the weakening of denitrification and anammox with the increase of aquifer depth. The reduction process consists of the enhancement of denitrification and anammox while the erosion of nitrification and ammonification with increased seawater intrusion. In addition, seawater intrusion can mitigate nitrate contamination by promoting denitrification and anammox in coastal areas.

Impact of environmental factors on diversity of fungi in sediments from the Shenzhen River Estuary

In this study, to explore the relationship between environmental factors and fungal diversity in the Shenzhen River ecosystem, multiple methods including chemical analysis, culture isolation, qPCR analysis of fungal ITS region and ITS-based Illumina next-generation-sequencing were integrated. A total of 115 isolates were finally isolated and could be classified into 23 genera. Top three abundant genera isolated were Meyerozyma (18 strains), Aspergillus (17 strains) and Penicillium (14 strains). Based on the Illumina sequencing approach, 829 OTUs were affiliated to seven phyla, 17 known classes, and 162 genera, indicating the Shenzhen estuary sediments are rich in fungal diversity. The major fungal genera were Meyerozyma, Trichoderma and Talaromyces. Environmental factors showed a gradient change in Shenzhen estuary, and fungal abundance was only significantly correlated with NH₄⁺. Shannon index was significantly correlated with pH and IC (P < 0.05). Principal coordinate analysis based on OTU level grouped into three clusters among sampling sites along with the IC and pH gradient. Functional guilds analysis suggests most of the fungi in this studying area were almost all saprotrophs, suggesting a large number of saprophytic fungi may play a significant role in the organic matter decomposition and nutrient cycling process. In summary, this study will deepen our understanding of fungi community in Shenzhen River ecosystem and their distribution and potential function shaped by environmental factors.

Wood vinegar facilitated growth and Cd/Zn phytoextraction of Sedum alfredii Hance by improving rhizosphere chemical properties and regulating bacterial community

Soil Cd and Zn contamination has become a serious environmental problem. This work explored the performance of wood vinegar (WV) in enhancing the phytoextraction of Cd/Zn by hyperaccumulator Sedum alfredii Hance. Rhizosphere chemical properties, enzyme activities and bacterial community were analyzed to determine the mechanisms of metal accumulation in this process. Results demonstrated that, after 120 days growth, different times dilution of WV increased the shoot biomass of S. alfredii by 85.2%-148%. In addition, WV application significantly increased soil available Cd and Zn by lowing soil pH, which facilitated plant uptake. The optimal Cd and Zn phytoextraction occurred from the 100 times diluted WV (D100), which increased the Cd and Zn extraction by 188% and 164%, compared to CK. The 100 and 50 times diluted WV significantly increased soil total and available carbon, nitrogen and phosphorus, and enhancing enzyme activities of urease, acid phosphatase, invertase and protease by 10.1-21.4%, 29.1-42.7%,12.2-38.3% and 26.8-85.7%, respectively, compared to CK. High-throughput sequencing revealed that the D 100 significantly increased the bacterial diversity compared to CK. Soil bacterial compositions at phylum, family and genera level were changed by WV addition. Compared to CK, WV application increased the relative abundances of genus with plant growth promotion and metal mobilization function such as, Bacillus, Gemmatimonas, Streptomyces, Sphingomonas and Polycyclovorans, which was positively correlated to biomass, Cd/Zn concentrations and extractions by S. alfredii. Structural equation modeling analysis showed that, soil chemical properties, enzyme activities and bacterial abundance directly or indirectly contributed to the biomass promotion, Cd, and Zn extraction by S. alfredii. To sum up, WV improved phytoextraction efficiency by enhancing plant growth, Cd and Zn extraction and increasing soil nutrients, enzyme activities, and modifying bacterial community.

Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient

Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.

Convergency and Stability Responses of Bacterial Communities to Salinization in Arid and Semiarid Areas: Implications for Global Climate Change in Lake Ecosystems

Climate change has given rise to salinization and nutrient enrichment in lake ecosystems of arid and semiarid areas, which have posed the bacterial communities not only into an ecotone in lake ecosystems but also into an assemblage of its own unique biomes. However, responses of bacterial communities to climate-related salinization and nutrient enrichment remain unclear. In September 2019, this study scrutinized the turnover of bacterial communities along gradients of increasing salinity and nutrient by a space-for-time substitution in Xinjiang Uyghur Autonomous Region, China. We find that salinization rather than nutrient enrichment primarily alters bacterial communities. The homogenous selection of salinization leads to convergent response of bacterial communities, which is revealed by the combination of a decreasing β-nearest taxon index (βNTI) and a pronounced negative correlation between niche breadth and salinity. Furthermore, interspecific interactions within bacterial communities significantly differed among distinct salinity levels. Specifically, mutualistic interactions showed an increase along the salinization. In contrast, topological parameters show hump-shaped curves (average degree and density) and sunken curves (modularity, density, and average path distance), the extremums of which all appear in the high-brackish environment, hinting that bacterial communities are comparatively stable at freshwater and brine environments but are unstable in moderately high-brackish lake.

Spatial variability pattern of the anaerobic ammonia-oxidizing bacterial community across a salinity gradient from river to ocean

In natural habitats, the diversity of anaerobic ammonia-oxidizing (anammox) bacteria could be affected by multiple environmental variables. In this study, we investigated the distribution of the anammox bacterial community in surface sediment from the Dongjiang River (riverine sediment, DJ) to the Pearl River Estuary (estuarine sediment, PRE) and then to the South China Sea (coastal sediment, SCS). The results revealed evident differences in the structural diversity of anammox bacteria in three different habitats. Candidatus Brocadia accounted for approximately 90% of the total anammox bacteria in DJ, conversely, Ca. Scalindua dominated in the SCS. Nevertheless, Ca. Scalindua, Ca. Brocadia and Ca. Kuenenia coexisted in the PRE. The qPCR results indicated that anammox bacterial 16S rRNA gene abundance ranged from 2.23 × 10⁵ to 1.19 × 10⁷ copies g^-1 of wet weight, but no significant correlation was found between the abundances and environmental variables (p > 0.05). The relative abundances of Ca. Brocadia gradually decreased with increasing salinity, and Ca. Scalindua showed the opposite trend, suggesting that salinity was a crucial factor in sculpturing the community composition of anammox bacteria in natural environments. Ca. Brocadia should be able to live in freshwater ecosystems, but it can also tolerate a certain level of salinity. Ca. Scalindua was halophilic anammox bacterium and exists only in saline environments. Ca. Kuenenia could adapt to a wide range of salinity and preferred to live in high DIN level conditions according to our search. The distribution pattern of anammox bacteria may be the result of microbial migration and long-term adaptation to salinity.

Influence of hydrological factors on bacterial community structure in a tropical monsoonal estuary in India

In the present study, we analyzed variations in bacterial community structure along a salinity gradient in a tropical monsoonal estuary (Cochin estuary [CE]), on the southwest coast of India, using Illumina next-generation sequencing (NGS). Water samples were collected from eight different locations thrice a year to assess the variability in the bacterial community structure and to determine the physico-chemical factors influencing the bacterial diversity. Proteobacteria was the most dominant phyla in the estuary followed by Bacteroidetes, Cyanobacteria, Actinobacteria, and Firmicutes. Statistical analysis indicated significant variations in bacterial communities between freshwater and mesohaline and euryhaline regions, as well as between the monsoon (wet) and nonmonsoon (dry) periods. The abundance of Betaproteobacteria was higher in the freshwater regions, while Alphaproteobacteria and Epsilonproteobactera were more abundant in mesohaline and euryhaline regions of the estuary. Gammaproteobacteria was more abundant in regions with high nutrient concentrations. Various bacterial genera indicating the presence of fecal contamination and eutrophication were detected. Corrplot based on Pearson correlation analysis demonstrated the important physico-chemical variables (temperature, salinity, dissolved oxygen, and inorganic nutrients) that influence the distribution of dominant phyla, class, and genera. The observed spatio-temporal variations in bacterial community structure in the CE were governed by regional variations in anthropogenic inputs and seasonal variations in monsoonal rainfall and tidal influx.

Abundance, community structure and diversity of nitrifying bacterial enrichments from low and high saline brackishwater environments

The study reports diversity in nitrifying microbial enrichments from low (0·5-5‰) and high (18-35‰) saline ecosystems. Microbial community profiling of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) enrichments was analysed by sequencing 16S rRNA and was processed using Mothur pipeline. The α-diversity indices showed the richness of nitrifying bacterial consortia from the high saline environment and were clustering based on the source of the sample. AOB and NOB enrichments from both the environments showed diverse lineages of phyla distributed in both groups with 38 and 34 phyla from low saline and 53 and 40 phyla in high saline sources, respectively. At class level, α- and γ-proteobacteria were found to be more dominant in both the enrichments. AOBs and NOBs in enrichments from low saline environments were dominated by Nitrosomonadaceae, Gallionellaceae (Nitrotoga sp.) and Ectothiorhodospiraceae and Nitrospira, respectively. Though Chromatiaceae were present in both AOB and NOB enrichments, Nitrosoglobus and Nitrosococcus dominated the AOBs while NOBs were dominated by uncultured genera, whereas Rhizobiales were found in both the enrichments. AOBs and NOBs in enrichments from high saline environments were dominated by Nitrospira-like AOBs, Nitrosomonas and Nitrosococcus genera, whereas ammonia-oxidizing archaea (AOA) group included Nitrosopumilus and Nitrososphaera genera comprising and Nitrospirae, respectively. The majority of the genera obtained in both the salinities were found to be either uncultured or unclassified groups. Results of the study suggest that the AOB and NOB consortia have unique and diverse microbes in each of the enrichments, capable of functioning in aquaculture systems practised at different salinities (0-60 ppt).

Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox

Few studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater

In this study, nitrification before and after abrupt cross-transfer in salinity was investigated in two moving bed biofilm reactors inoculated with nitrifying cultures that had adaptation to freshwater (FR) and seawater salinities (SR). FR and SR MBRRs were exposed to short and long term cross-transfer in salinity, and the functional capacity of nitrifying microbial communities was quantified by the estimation of ammonia and nitrite oxidation rates. Salinity induced successions were evaluated before and after salinity change by deep sequencing of 16S rRNA gene amplicons and statistical analysis. The bacterial community structure was characterized and Venn diagrams were included. The results indicated that after salinity cross-transfer, the FR was not significantly recovered at seawater salinity whereas SR showed high resistance to stress caused by low-salt. Succession and physiological plasticity were the main mechanisms of the long-term adaption of the nitrifying communities exposed to abrupt salinity changes. Independently of salinity, some nitrifiers presented high physiological plasticity towards salinity and were very successful at both zero and full seawater salinity. SR culture is robust and suitable inoculum for ammonium removal from recirculating aquaculture systems and industrial wastewaters with variable and fast salinity changes. Our findings contradict the current perspective of the significance of salinity on the structure of nitrifying communities.

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

Characteristics of chlorinated and brominated polycyclic aromatic hydrocarbons in the Pearl River Estuary

The spatial distribution of halogenated polycyclic aromatic hydrocarbons (H-PAHs) (8 chlorinated PAHs (Cl-PAHs) and 9 brominated PAHs (Br-PAHs)), in the Pearl River Estuary (PRE) was investigated. The total concentrations of 17H-PAHs in sediment samples were ranged from 1.4 ng g^-1 to 40.9 ng g^-1 with an average concentration of 14.7 ng g^-1. The average H-PAH concentration in the suspended particulate matters (SPMs) (475.6 ng g^-1) was 30 times higher than that in the sediments (14.7 ng g^-1), and H-PAHs were rarely detected in the aqueous phase. The dominant H-PAHs in sediments were 9,10-dichloroanthracene (31.2%) and 9-chlorophenanthrene (32.0%); 2/9-chlorofluorene (27.4%) was prominent in surface SPMs, while no significant dominant congeners were found in bottom SPMs. Principal component analysis showed that the congener profiles of H-PAHs in sediments were different from those of SPMs especially for surface SPM samples which might be caused by point source discharges of H-PAHs from the coast of the PRE. In general, riverine inputs were the major source of H-PAHs in the PRE, and SPMs were important carriers for transporting H-PAHs. Diagnostic analyses showed that the H-PAHs might originate from waste incineration and automobile emissions in the Pearl River Delta (PRD).

Influence of salinity stress on bacterial community composition and β-glucosidase activity in a tropical estuary: Elucidation through microcosm experiments

The influence of changing salinity on community composition and functional activity (Bacterial Production (BP) and ectoenzyme activity) of major bacterial taxa was evaluated using microcosm experiments in a tropical monsoon influenced estuary. Natural bacterial inocula at different salinities, representing marine, brackish, and freshwater, were inter-transferred and elucidated their response with an emphasis on community composition and β-Glucosidase (BGase) activity. The results revealed a significant decrease in the total bacterial count (TBC) and BP on the translocation of bacterial inocula to different salinity conditions in the case of freshwater bacteria. However, a significant increase in BGase activity coupled with shifts in the studied bacterial groups was evident in the case of marine as well as freshwater bacteria. Quantitative PCR (qPCR) revealed a shift in major bacterial taxa upon translocation to different waters, which was dependent on salinity and the source of inocula. Redundancy and qPCR analyses showed that members belonging to Gammaproteobacteria and Betaproteobacteria were higher, and possibly influenced BGase activity in marine and freshwater, respectively. Translocation of marine inocula to brackish and freshwater resulted in an emergence of Bacteroidetes, Actinobacteria, and Betaproteobacteria, respectively. Whereas, when freshwater inocula were translocated to marine or brackish water, Alphaproteobacteria and Gammaproteobacteria taxa emerged, and this was coupled with increased BGase activity. In contrast, brackish water bacteria showed a strong persistence in bacterial community composition when translocated to different salinities within this estuary. Such phylogenetic persistence or changes suggests species level shifts in specific bacterial taxa, and unravelling the same using different functional gene markers would ascertain their role in organic matter processing and is way forward.

Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai-Tibetan Plateau

In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai-Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g-1 and 9.73 × 103 copies g-1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions.

Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary

Purpose

The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.

Result

The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.

Conclusions

The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.

The roles of environmental variation and spatial distance in explaining diversity and biogeography of soil denitrifying communities in remote Tibetan wetlands

The relative importance of local environments and dispersal limitation in shaping denitrifier community structure remains elusive. Here, we collected soils from 36 riverine, lacustrine and palustrine wetland sites on the remote Tibetan Plateau and characterized the soil denitrifier communities using high-throughput amplicon sequencing of the nirS and nirK genes. Results showed that the richness of nirS-type denitrifiers in riverine wetlands was significantly higher than that in lacustrine wetlands but not significantly different from that in palustrine wetlands. There was no clear distinction in nir community composition among the three kinds of wetlands. Irrespective of wetland type, the soil denitrification rate was positively related to the abundance, but not the α-diversity, of denitrifying communities. Soil moisture, carbon availability and soil temperature were the main determinants of diversity [operational taxonomic unit (OTU) number] and abundance of thenirS-type denitrifier community, while water total organic carbon, soil NO3- and soil moisture were important in controlling nirK-type denitrifier diversity and abundance. The nirS community composition was influenced by water electrical conductivity, soil temperature and water depth, while the nirK community composition was affected by soil electrical conductivity. Spatial distance explained more variation in the nirS community composition than in the nirK community composition. Our findings highlight the importance of both environmental filtering and spatial distance in explaining diversity and biogeography of soil nir communities in remote and relatively undisturbed wetlands.

Recovery of the benthic bacterial community in coastal abandoned saltern requires over 35 years: A comparative case study in the Yellow Sea

Salt is an essential nutrient for humans, and salterns exist worldwide. Although the construction of salterns has stopped and typical salterns are now mostly abandoned, there has been no research on the ecological recovery of the abandoned salterns. Here, we analyzed the bacterial diversity and community structure in three pairs of abandoned salterns that have undergone 1-35 years of natural restoration and tidal flats to determine the recovery time and process. Partial 16S rRNA sequences were amplified and sequenced to investigate the biodiversity and structure of the bacterial community in sediments collected from abandoned salterns and adjacent natural tidal flats (viz., controls) in the Yellow Sea. The most abundant microorganisms across locations were found to be members of Proteobacteria, ranging from 45 to 72%, which was also a crucial taxon in the bacterial recovery process. The benthic bacterial community of the salterns showed time-dependent recovery, as demonstrated by the similarity between the salterns and controls. Indeed, dissimilarities between bacterial communities were significant for the saltern that had been abandoned for one year, according to ANOSIM (R = 1.0, p < 0.01). The genera that were determined to contribute to the dissimilarity exhibited a significant correlation with the sedimentary phosphorus concentration. The dataset generally supported that the indigenous benthic bacterial community in an altered marine environment might require a considerable time to return to a natural status. Meanwhile, a delay between the recovery of the physicochemical environment and biological component was evidenced, which seemed to influence the recovery time in a site-specific manner. Overall, the present study provided new insight and understanding of the recovery of the benthic bacterial community in abandoned salterns in terms of recovery time and the associated process.

Influence of local and regional drivers on spatial and temporal variation of ammonia-oxidizing communities in Gulf of Mexico salt marshes

We characterized ammonia-oxidizing archaea (AOA) and bacteria (AOB) from salt marsh sediments in the Gulf of Mexico over 5 years to identify environmental drivers of nitrifying community patterns following the Deepwater Horizon oil spill. Samples were collected from oiled and unoiled sites in July of 2012-2016 from 12 marshes spanning three regions on the Louisiana coast. No consistent oil effect was detected for either AOA or AOB abundance or community composition. At the local scale, abundance was correlated with changes in marsh elevation, suggesting that oxygen may be an important driver. Regional differences in abundance were best explained by salinity and soil moisture, while interannual variation may be more linked to changes in climate and Mississippi River discharge. Variation of AOA communities was correlated with organic sediment nutrients, while AOB communities were correlated with soil extractable nutrients. AOA and AOB diversity and AOB abundance decreased in 2014 in all regions, suggesting that broad-scale drivers, such as climate, may explain synchronous shifts throughout the coastal area. Our results provide insights about large-scale disturbances on nitrifying microbes in the Gulf of Mexico, and suggest that nitrogen cycling may be controlled primarily by local factors, but large-scale drivers might override these localized differences at times.

Impacts of Freshwater and Seawater Mixing on the Production and Decay of Virioplankton in a Subtropical Estuary

Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments. In PRE, viral abundance, production and decay rates varied from 2.72 ± 0.09 to 27.5 ± 1.07 × 10⁶ viruses ml^-1, 7.98 ± 2.33 to 16.27 ± 2.85% h^-1 and 0.80 ± 0.23 to 3.74 ± 0.98% h^-1, respectively. When the riverine and marine microbial community were transferred into simulated brackish water, viral production rates were markedly inhibited by 83.8% and 47.3%, respectively. The decay of riverine and marine virioplankton was inhibited by 21.1% and 34.2%, respectively, in simulated brackish water. These results indicate change of estuarine environmental factors significantly alters the dynamics of riverine and marine virioplankton. In addition, the effects of mixing on viral production and decay differed between high- and low-fluorescence viruses. High-fluorescence viruses seemed more resistant to decay than low-fluorescence viruses, whereas the production of marine low-fluorescence viruses seemed more resistant to inhibition than that of marine high-fluorescence viruses. Together, these results provide new insights into the ecological dynamics of virioplankton in estuarine environments.

Anthropogenic impact on nitrification dynamics in coastal waters of the Mediterranean Sea

The anthropogenic alteration of the nitrogen cycle results in the modification of the whole food web. And yet, the impact caused on nitrogen dynamics in marine systems is still very uncertain. We propose a workflow to evaluate changes to coastal nitrification by modelling nitrite dynamics, the intermediary compound. Nitrite concentrations were estimated with a simple steady state nitrification model, which was calibrated in 9 NW Mediterranean coastal sites with different anthropogenic pressures, located within 250 km. The results obtained indicate that nitrite peaks are observed in winter and explained by nitrification response to temperature, but these dynamics are altered in impacted coastal waters. We found the second step of nitrification to be more sensitive to temperature, which entails a significant impact of climate change on the decoupling of the two steps of nitrification. The results could be extrapolated to numerous coastal regions of the Mediterranean Sea with similar characteristics.

Mudflat reclamation causes changes of gene abundance in nitrogen cycle under long-term rice cultivation

Rice cultivation is the main method for mudflat reclamation. However, changes in the community structure of microbes involved in nitrogen (N) cycling in response to mudflat reclamation via rice cultivation remain poorly understood. This study used quantitative polymerase chain reaction to characterize the distribution of various inorganic N-cycling pathways in response to mudflat reclamation via rice cultivation. The results show that the abundance of functional genes followed an increasing trend, while the relative abundance showed a decreasing trend. The relative richness of functional genes in the inorganic N-cycling network showed different fluctuation trends and indicated that the nifH, archaea amoA, narG, nirS, nirK, norB, and nosZ genes greatly contribute to inorganic N-cycling. Redundancy analysis showed that soil properties, in particular, organic matter increased, while electrical conductivity decreased, driving the changes of gene distribution in the inorganic N-cycling network over the course of reclamation. Mudflat reclamation under long-term rice cultivation promoted the reproduction of microbes related to the N cycle, and also changed the distribution of functional genes that are involved in the inorganic N cycle due to changes of soil properties.

Community composition of marine and brackish water ammonia-oxidizing consortia developed for aquaculture application

To mitigate the toxicity of ammonia in aquaculture systems, marine and brackish water ammonia-oxidizing bacterial consortia have been developed and are used for activation of nitrifying bioreactors integrated to recirculating aquaculture systems. To shed more light on to these biological entities, diversity of both the consortia were analyzed based on random cloning of 16S rRNA gene and ammonia-oxidizing bacterial specific amoA gene sequences. The dendrograms of representative clones on the basis of amplified ribosomal DNA restriction analysis generated 22 and 19 clusters for marine and brackish water nitrifying consortia, respectively. Phylogenetic analysis demonstrated the presence of various autotrophic nitrifiers belonging to α-, β- and γ-Proteobacteria, anaerobic ammonia oxidizers, heterotrophic denitrifiers, Bacteroidetes, and Actinobacteria. Distribution patterns of the organisms within the two consortia were determined using the software Geneious and diversity indices were investigated using Mega 5.0, VITCOMIC and Primer 7. The abundance of ammonia oxidizers was found in the order of 2.21 ± 0.25 × 10⁹ copies/g wet weight of marine consortium and 6.20 ± 0.23 × 10⁷ copies/g of brackish water consortium. Besides, marine ammonia-oxidizing consortium exhibited higher mean population diversity and Shannon Wiener diversity than the brackish water counterparts.

Organic matter decomposition sustains sedimentary nitrogen loss in the Pearl River Estuary, China

The Pearl River Estuary (PRE) has long received tremendous amounts of anthropogenic nitrogen, and is facing severe environmental problems. Denitrification and anaerobic ammonium oxidation (anammox) are known to be two major nitrogen removal pathways in estuarine sediments. Through the use of slurry and intact sediment core incubations, we examined the nitrogen removal pathways and quantified the in situ denitrification and anammox with associated gaseous nitrogen production rates. Sedimentary nitrogen removal was predominated by denitrification (93-100%) relative to a minimal contribution (<7%) from anammox. Among the detected environmental factors, salinity, bottom water NO_x^- (nitrate and nitrite) concentration, sedimentary organic matter and dissolved oxygen consumption rates showed good correlations with denitrification and anammox rates. Sedimentary nitrogen loss was mainly supported by endogenic coupled nitrification-denitrification (6.0 ± 1.5 × 10⁶ mol N d^-1), with water-column-delivered NO_x^- (2.1 ± 0.6 × 10⁶ mol N d^-1) as the secondary source. Such results suggested that sedimentary nitrogen removal involved mainly particulate organic form (allochthonous or autochthonous) deposited onto sediments, rather than inorganic forms in overlying water. Meanwhile, total N₂O production from sediments was estimated to be 7.3 ± 2.1 × 10⁴ mol N d^-1, equivalent to ~35% of the daily N₂O emissions in the PRE.

Nitrogen cycling during wastewater treatment

Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.

Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China

Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers' distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers' communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers' community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers' community compositions.

Effect of salinity on soil respiration in relation to dissolved organic carbon and microbial characteristics of a wetland in the Liaohe River estuary, Northeast China

Increasing salinity has important impacts on biogeochemical processes in estuary wetlands, with the potential to influence the soil respiration, dissolved organic carbon (DOC) and microbial population. However, it is unclear how soil respiration is related to changes in the DOC and microbial community composition with increasing salinity. In this study, soil cores were sampled from a brackish wetland in the Liaohe River estuary and treated by salinity solutions at four levels (fresh water, 3‰, 5‰, and 10‰). Samples of gas, water and soil were collected to determine the respiration rates and microbial community structure of the soil and the DOC leaching from the soil. Compared to the low-salinity treatments (fresh water and 3‰), the high-salinity treatments (5‰ and 10‰) decreased the soil respiration rates by 45-57% and decreased the DOC concentrations by 47-55%. However, no significant differences were observed within the low-salinity treatments nor the high-salinity treatments. There is a positive correlation between the soil respiration rates and DOC concentrations in all treatments, but it does not indicate a genetic cause-effect relationship between them. The microbial community structure varied with the salinity level, with higher β- and δ-Proteobacteria abundance, as well as higher Anaerolineae, and lower Clostridia abundance in the high-salinity treatments. The respiration rates were slightly negatively related to the richness of Proteobacteria and positively related to the richness of Clostridia. This study suggests that there may be a salinity threshold (3-10‰) impacting the organic carbon loss from estuarine brackish wetlands. In addition, the response of soil respiration to increasing salinity may be mainly linked to changes in the microbial community composition rather than changes in the DOC quantity.

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach

This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses.

Water Salinity Should Be Reduced for Irrigation to Minimize Its Risk of Increased Soil N₂O Emissions

To reveal the effect of irrigation salinity on soil nitrous oxide (N₂O) emission, pot experiments were designed with three irrigation salinity levels (NaCl and CaCl₂ of 1, 2.5 and 4 g/L equivalence, Ec = 3.6, 8.1 and 12.7 ds/m), either for 0 kg N/ha (N0) or 120 kg N/ha (N120) nitrogen inputs. N₂O emissions from soils irrigated at different salinity levels varied in a similar pattern which was triggered by soil moisture dynamics. Yet, the magnitudes of pulse N₂O fluxes were significantly varied, with the peak flux at 5 g/L irrigation salinity level being much higher than at 2 and 8 g/L. Compared to fresh water irrigated soils, cumulative N₂O fluxes were reduced by 22.7% and 39.6% (N0), 29.1% and 39.2% (N120) for soils irrigated with 2 and 8 g/L saline water, while they were increased by 87.7% (N0) and 58.3% (N120) for soils irrigated with 5 g/L saline water. These results suggested that the effect degree of salinity on consumption and production of N₂O might vary among irrigation salinity ranges. As such, desalinating brackish water to a low salinity level (such as 2 g/L) before it is used for irrigation might be helpful for solving water resources crises and mitigating soil N₂O emissions.

Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS). Nitrosopumilus (AOA) and Nitrosospira (AOB) were predominant lineages, but their abundances varied significantly between ECS, and BS and YS. This was mainly attributed to salinity and dissolved oxygen of the bottom water. The discovery of a high abundance of Nitrosophaera at estuarine sites suggested strong terrigenous influence exerted on the AOA community. In contrast, variations in ocean conditions played more important roles in structuring the AOB community, which was separated by bottom water dissolved oxygen into two groups: the south YS, and the north YS and BS. This study provides a comprehensive insight into the spatial distribution pattern of ammonia-oxidizing prokaryotes in ECMS sediments, laying a foundation for understanding their relative roles in nitrification.

Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments

Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.

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.

Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence

Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed salt marsh chronosequence spanning over a century of ecosystem development to investigate changes in the community composition and abundance of a set of nitrogen-cycling genes. Specifically, we targeted genes of diazotrophs and ammonia oxidizers associated with the bulk and rhizosphere soil of the plant species Limonium vulgare. Samples were collected across five distinct successional stages of the chronosequence (ranging from 5 to 105 years) at two time-points. Our results indicate that soil variables such as sand:silt:clay % content and pH strongly relates to the abundance of N-cycling genes in the bulk soil. However, in the rhizosphere samples, the abundance of ammonia-oxidizing organisms (both bacteria and archaea, AOB and AOA, respectively) was relatively constant across most of the successional stages, albeit displaying seasonal variation. This result indicates a potentially stronger control of plant host (rather than soil) on the abundance of these organisms. Interestingly, the plant host did not have a significant effect on the composition of AOA and AOB communities, being mostly divergent according to soil successional stages. The abundance of diazotrophic communities in rhizosphere samples was more affected by seasonality than those of bulk soil. Moreover, the abundance pattern of diazotrophs in the rhizosphere related to the systematic increase of plant biomass and soil organic matter along the successional gradient. These results suggest a potential season-dependent regulation of diazotrophs exerted by the plant host. Overall, this study contributes to a better understanding of how the natural formation of a soil and host plants influence the compositional and abundance changes of nitrogen-cycling genes in bulk and rhizosphere soil microhabitats.

Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.

Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China

Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.

Effects of salinity on the denitrification efficiency and community structure of a combined partial nitritation- anaerobic ammonium oxidation process

The effects of salinity changes on nitrogen transformation efficiency and recoverability were studied by using a partial nitration (PN)- anaerobic ammonium oxidation (Anammox) integrated reactor. The changes of microbial community structure and population abundance during the increase and decrease of salinity were also analyzed by 16S rRNA gene high-throughput sequencing. The results showed that when the salinity was increased to 1.35%, the combined PN-Anammox process achieved the maximum stimulated and total nitrogen removal rate (TNRR) arrived at 1.1kg/(m³·d). When the salinity was higher than 1.35%, the activities of AOB and Anammox bacteria began to be inhibited. When the salinity reached 2.4%, the TNRR decreased to 60%. TNRR was fast restored, when salinity was reduced to 0.11%. The genes of AOB and Anammox bacteria indicated that the TNRR of the reactor was restored after salinity inhibition, but the functional microbial community structure and abundance had relatively large, irreversible changes.

nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary

Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe²⁺ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H₂ S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function.

Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments

In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH₄⁺ but lower concentrations of both NO₂^- and NO₃^-, and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH₄⁺ and NO₂^- were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.

Spatiotemporal variability in salinity and hydraulic relationship with salt intrusion in the tidal reaches of the Minjiang River, Fujian Province, China

Salinity is one of the most important factors for tidal-affected water bodies including estuaries and tidal river reaches. However, due to the limitations of simultaneous manual monitoring in long-distance areas, studies of estuaries are preferred to tidal reaches. Hence, in this study, we investigated the tidal reach of the Minjiang River and five sets of field observations were used to determine the influence of saltwater intrusion in different seasons. During the dry and wet season with low discharge, the longitudinal salinity profiles showed that a station located about 45 km from the river mouth still suffered from saltwater intrusion especially when the upstream discharge was under 754 m³ s^-1, where the periodical fluctuation in the salinity remained the same with the water level, but there was a time lag of approximately 4 h compared with the discharge process. However, during the wet season in April and May 2016, the monitored salinity was approximately at the detectable limit of 0.02-0.04 ppt at the station close to the river mouth, which indicated that there was no saltwater exchange into the river, although dual flow directions were observed in the survey periods. The major differences among five survey periods were mainly related to upstream discharge rather than the seasons, the tidal range, and tidal excursion. The conclusions of this study have strategic importance for protecting water sources by guiding the government to assess the optimal freshwater release time and discharge rate to prevent saltwater entering the important tidal-affected river reaches.