Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China

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.

Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process

Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.

Unveiling the impact and mechanisms of Cd-driven ecological assembly and coexistence of bacterial communities in coastal sediments of Yellow Sea

The microbial community assembly processes and underlying mechanisms in response to heavy metal accumulation in coastal sediments remain underexplored. In this study, the heavy metal concentration in samples were found below the marine sediment quality standards. Through partial Mantel tests and linear regression analysis, Cd was identified as the major influencing factor, displaying strongest correlation with the bacterial community in the sediments. The class Desulfuromonadia was identified as a biomarker which showed enrichment in the sediments with high Cd content. Additionally, the results of null model and the neutral community model demonstrated the prominent role of stochastic processes in the assembly of bacterial community. However, with the increase in Cd concentration, the influence of selection processes intensified, resulting in a decline in species migration rate and subsequent reduction in ecological niche width. Furthermore, the intensified competition and an increase in keystone species among bacterial populations further enhanced the stability of the microbial co-occurrence network in response to high Cd concentration. This study offers an insight into the effects of heavy metal on microbial assembly and coexistence, which are conducive to marine ecosystem management and conservation.

Microbial machinery dealing diverse aromatic compounds: Decoded from pelagic sediment ecogenomics in the gulfs of Kathiawar Peninsula and Arabian Sea

Aromatic hydrocarbons are persistent pollutants in aquatic systems as endocrine disruptors, significantly impacting natural ecosystems and human health. Microbes perform as natural bioremediators to remove and regulate aromatic hydrocarbons in the marine ecosystem. The present study focuses upon the comparative diversity and abundance of various hydrocarbon-degrading enzymes and their pathways from deep sediments along the Gulf of Kathiawar Peninsula and Arabian Sea, India. The elucidation of large number of degradation pathways in the study area under the presence of a wide range of pollutants whose fate needs to be addressed. Sediment core samples were collected, and the whole microbiome was sequenced. Analysis of the predicted ORFs (open reading frames) against the AromaDeg database revealed 2946 aromatic hydrocarbon-degrading enzyme sequences. Statistical analysis portrayed that the Gulfs were more diverse in degradation pathways compared to the open sea, with the Gulf of Kutch being more prosperous and more diverse than the Gulf of Cambay. The vast majority of the annotated ORFs belonged to groups of dioxygenases that included catechol, gentisate, and benzene dioxygenases, along with Rieske (2Fe-2S) and vicinal oxygen chelate (VOC) family proteins. From the sampling sites, only 960 of the total predicted genes were given taxonomic annotations, which mention the presence of many under-explored marine microorganism-derived hydrocarbon degrading genes and pathways. Through the present study, we tried to unveil the array of catabolic pathways of aromatic hydrocarbon degradation and genes from a marine ecosystem that upholds economic and ecological significance in India. Thus, this study provides vast opportunities and strategies for microbial resource recovery in marine ecosystems, which can be investigated to explore aromatic hydrocarbon degradation and their potential mechanisms under various oxic or anoxic environments. Future studies should focus on aromatic hydrocarbon degradation by considering degradation pathways, biochemical analysis, enzymatic, metabolic, and genetic systems, and regulations.

Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments

Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of available nitrogen. At three sediment depths (0-1; 1-5; 5-10 cm) across a 2 year study key genes involved in nitrification (archaeal amoA and bacterial β-amoA), nitrite reduction (clade I nirS and cluster I nirK, archaeal nirK-a), anaerobic oxidation of ammonium (anammox 16S rRNA phylogenetic marker) and nitrogen fixation (nifH) were quantified. Sediments impacted by a dominance of organic nitrogen inputs were characterised at all time-points and to sediment depths of 10 cm by the highest transcript abundances of archaeal amoA and archaeal nirk-a. Proximity to a dominance of external nitrate inputs was associated with the highest transcript abundances of nirS which temporally co-varied with seasonal changes in sediment nitrate. Sediments isolated from external inputs displayed the greatest depth-specific decrease in quantifiable transcript abundances. In these isolated sediments bacterial β-amoA transcripts were temporally associated with increased sediment ammonium levels. Across this nitrogen limited system variability in the abundance of bacterial β-amoA, archaeal amoA, archaeal nirk-a or nirS transcripts from the sediment surface (0-1 and 5 cm) demonstrated a capacity to improve our ability to monitor coastal zones impacted by anthropogenic nitrogen inputs. Specifically, the spatial detection sensitivity of bacterial β-amoA transcripts could be developed as a metric to determine spatiotemporal impacts of large external loading events. This temporal study demonstrates a capacity for microbial activity metrics to facilitate coastal management strategies through greater spatial resolution of areas impacted by external nutrient inputs.

Effects of Bradyrhizobium Co-Inoculated with Bacillus and Paenibacillus on the Structure and Functional Genes of Soybean Rhizobacteria Community

Plant growth-promoting rhizobacteria (PGPR) are widely used to improve soil nutrients and promote plant growth and health. However, the growth-promoting effect of a single PGPR on plants is limited. Here, we evaluated the effect of applying rhizobium Bradyrhizobium japonicum 5038 (R5038) and two PGPR strains, Bacillus aryabhattai MB35-5 (BA) and Paenibacillus mucilaginosus 3016 (PM), alone or in different combinations on the soil properties and rhizosphere bacterial community composition of soybean (Glycine max). Additionally, metagenomic sequencing was performed to elucidate the profile of functional genes. Inoculation with compound microbial inoculant containing R5038 and BA (RB) significantly improved nodule nitrogenase activity and increased soil nitrogen content, and urease activity increased the abundance of the nitrogen cycle genes and Betaproteobacteria and Chitinophagia in the rhizosphere. In the treatment of inoculant-containing R5038 and PM (RP), significant changes were found for the abundance of Deltaproteobacteria and Gemmatimonadetes and the phosphorus cycle genes, and soil available phosphorus and phosphatase activity were increased. The RBP inoculants composed of three strains (R5038, BA and PM) significantly affected soybean biomass and the N and P contents of the rhizosphere. Compared with RB and RP, RBP consistently increased soybean nitrogen content, and dry weight. Overall, these results showed that several PGPR with different functions could be combined into composite bacterial inoculants, which coordinately modulate the rhizosphere microbial community structure and improve soybean growth.

Effects of Land Use on the Soil Microbial Community in the Songnen Grassland of Northeast China

Land use change obviously changes the plant community composition and soil properties of grasslands and thus affects multiple functions and services of grassland ecosystems. However, the response mechanisms of soil microorganisms, key drivers of the nutrient cycle and other soil functions during changes in grassland use type and associated vegetation are not well understood. In this study, Illumina high-throughput sequencing was used to analyze the changes in the soil microbial community structure of four grassland use types: exclosure (EL), mowed land (ML), grazed land (GL), and farmland (FL) in the Songnen Plain of Northeast China. The results showed that the FL and EL had significantly higher soil total nitrogen (TN) and lower soil electrical conductivity (EC) and pH than GL and ML. In contrast, the GL and ML had higher soil bulk density (BD) and organic matter, respectively, than the other land use types. In addition, the values of the Shannon diversity and Pielou’s evenness indexes were highest in the EL of all the land use types. Based on the high-throughput sequencing results, we observed high levels of α diversity in the FL for both bacteria and fungi. A structural equation model (SEM) revealed that pH and EC had a direct and positive effect on the bacterial community structure and composition. In addition, plant taxonomic diversity (according to the Shannon diversity and Pielou’s evenness indexes) indirectly affected the bacterial community composition via soil pH and EC. Notably, fungal composition was directly and positively correlated with soil nutrients and the value of Pielou’s evenness index changed with land use type. In conclusion, soil properties and/or plant diversity might drive the changes in the soil microbial community structure and composition in different grassland use types.

Microbial diversity and community structure in deep-sea sediments of South Indian Ocean

Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.

Lake microbiome and trophy fluctuations of the ancient hemp rettery

Lake sediments not only store the long-term ecological information including pollen and microfossils but are also a source of sedimentary DNA (sedDNA). Here, by the combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedDNA we were able to paint a comprehensive picture of the fluctuations in trophy and bacterial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of the Roman and Early Medieval periods and correlated these to the increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply—hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest the employment of the fibre count analysis as an additional and independent proxy.

Study on the properties of denitrifying carbon sources from cellulose plants and their nitrogen removal mechanisms

Carbon sources of cellulose plants are promising materials that enhance the activities of denitrifying bacteria in the groundwater system. To further verify the denitrification performance of cellulose plants and the main factors of affecting the denitrifying system, six cellulose plants from agricultural wastes (wood chip, corn cob, rice husk, corn straw, wheat straw, and sugar cane) were selected for bioavailable organic matter leaching experiments, carbon denitrification experiments, functional bacteria identification, and analysis experiments. The results show that the extracts of cellulose plants contain a mixed carbon sources system including small molecular organic acids, sugars, nitrogen-containing organic components, and esters. The qPCR results showed that the denitrifying bacteria had obvious advantages compared to anaerobic ammonia-oxidizing bacteria during the stable period; the denitrification experiment showed that each of six cellulose plants removed more than 80% of nitrogen, and the denitrification rates reached 1.00-2.00 mg N cm^-3·d^-1. The supplement of cellulose plants promotes the metabolism rate of denitrifying bacteria, and the additional denitrifying bacteria have little effect on nitrate removal. In summary, the expected denitrification reaction occurred in the cellulose plant system, which is suitable as a carbon source material for water body nitrogen pollution remediation.

Diversity, abundance, and distribution of anammox bacteria in shipping channel sediment of Hong Kong by analysis of DNA and RNA

Anammox bacteria have been detected in various ecosystems, but their occurrence and community composition along the shipping channels have not been reported. In this study, anammox bacteria were recovered by PCR-amplified biomarker hzsB gene from the genomic DNA of the sediment samples. Phylogenetic tree revealed that Candidatus Scalindua and Ca. Brocadia dominated the anammox community of the Hong Kong channels; Ca. Scalindua spp. was present abundantly at the sites farther from the shore, whereas Ca. Jettenia and Ca. Kuenenia were detected as the minor members in the estuarine sediments near the shipping terminals. The highest values of Shannon-Wiener index and Chao1 were identified in the sediments along the Urmston road (UR), suggesting the highest α-diversity and species richness of anammox bacteria. PCoA analysis indicated that anammox bacterial communities along UR and Tai Hong (TH) channel were site-specific because these samples were grouped and clearly separated from the other samples. The maximum diversity of anammox bacteria was detected in UR samples, ranging from 6.28 × 10⁵ to 1.28 × 10⁶ gene copies per gram of dry sediment. A similar pattern of their transcriptional activities was also observed among these channels. Pearson's moment correlation and redundancy analysis indicated that NH₄⁺-N was a strong factor shaping the community structure, which showed significant positive correlation with the anammox bacterial abundance and anammox transcriptional activities (p < 0.01, r > 0.8). Also, NH₄⁺-N, (NO₃^- + NO₂^-)-N, and NH₄⁺/NO_X were additional key environmental factors that influenced the anammox community diversity and distribution. This study yields a better understanding of the ecological distribution of anammox bacteria and the dominant genera in selective niche.

Saline and alkaline stresses alter soil properties and composition and structure of gene-based nitrifier and denitrifier communities in a calcareous desert soil

BACKGROUND

Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the responses of gene-based nitrifier and denitrifier communities to chloride (CS), sulfate (SS), and alkaline (AS) stresses with those in a no-stress control (CK) in pots with a calcareous desert soil.

RESULTS

Compared with CK, saline and alkaline stress decreased potential nitrification rate (PNR) and NO₃-N; increased pH, salinity, water content, and NH₄-N; and decreased copy numbers of amoA-AOA and amoA-AOB genes but increased those of denitrifier nirS and nosZ genes. Copies of nirK increased in SS and AS but decreased in CS. There were more copies of amoA-AOB than of amoA-AOA and of nirS than of nirK or nosZ. Compared with CK, SS and AS decreased operational taxonomic units (OTUs) of amoA-AOB but increased those of nirS and nosZ, whereas CS decreased nirK OTUs but increased those of nosZ. The numbers of OTUs and amoA-AOB genes were greater than those of amoA-AOA. There were positive linear relations between PNR and amoA-AOA and amoA-AOB copies. Compared with CK, the Chao 1 index of amoA-AOA and amoA-AOB decreased in AS, that of nirK increased in CS and SS, but that of nirS and nosZ increased in all treatments. The Shannon index of amoA-AOB decreased but that of nirS increased in CS and SS, whereas the index of nirK decreased in all treatments. Saline and alkaline stress greatly affected the structure of nitrifier and denitrifier communities and decreased potential biomarkers of nirS-type; however, AS increased those of nirK- and nosZ-type, and SS decreased those of nosZ-type. Soil water content, pH, and salinity were important in shaping amoA-AOA and denitrifier communities, whereas soil water and pH were important to amoA-AOB communities.

CONCLUSION

These results indicate that the nitrifier and denitrifier communities respond to saline and alkaline stresses conditions. Communities of amoA-AOA and amoA-AOB contribute to nitrification in alluvial gray desert soil, and those of nirS are more important in denitrification than those of nirK or nosZ.

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.

Genetic Diversity, Community Assembly, and Shaping Factors of Benthic Microbial Eukaryotes in Dongshan Bay, Southeast China

Microbial eukaryotes are pivotal components of marine ecosystems. However, compared with the pelagic environments, the diversity distribution and the driving mechanisms of microbial eukaryotes in the marine sediments have rarely been explored. In this study, sediment cores were collected along a transect from inner to outer Dongshan Bay, Southeast China. By combining high throughput sequencing of small-subunit (SSU) rRNA gene with measurements on multiple environmental variables, the genetic diversity, community structure and assembly processes, and environmental shaping factors were investigated. Alveolata (mainly Ciliophora and Dinophyceae), Rhizaria (mainly Cercozoa), and Stramenopiles (mainly Bacillariophyta) were the most dominant groups in terms of both relative sequence abundance and operational taxonomic unit (OTU) richness. Grain size composition of the sediment was the primary factor determining the alpha diversity of microbial eukaryotes followed by sediment depth and heavy metal, including chromium (Cr), zinc (Zn), and plumbum (Pb). Geographic distance and water depth surpassed other environmental factors to be the primary factors shaping the microbial eukaryotic communities. Dispersal limitation was the primary driver of the microbial eukaryotic communities, followed by drift and homogeneous selection. Overall, our study shed new light on the spatial distribution patterns and controlling factors of benthic microbial eukaryotes in a subtropical bay which is subjected to increasing anthropogenic pressure.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Monthly distribution of ammonia-oxidizing microbes in a tropical bay

Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17-20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17-20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.

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.

Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China

Complete ammonia oxidizers (comammox), able to individually oxidize ammonia to nitrate, are considered to play a significant role in the global nitrogen cycle. However, the distribution of comammox Nitrospira in estuarine tidal flat wetland and the environmental drivers affecting their abundance and diversity remain unknown. Here, we present a large-scale investigation on the geographical distribution of comammox Nitrospira along the estuarine tidal flat wetlands of China, where comammox Nitrospira were successfully detected in 9 of the 16 sampling sites. The abundance of comammox Nitrospira ranged from 4.15 × 10⁵ to 6.67 × 10⁶ copies/g, 2.21- to 5.44-folds lower than canonical ammonia oxidizers: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Phylogenetic analysis based on the alpha subunit of the ammonia monooxygenase encoding gene (amoA) revealed that comammox Nitrospira Clade A, mainly originating from upstream river inputs, accounts for more than 80% of the detected comammox Nitrospira, whereas comammox Nitrospira clade B were rarely detected. Comammox Nitrospira abundance and dominant comammox Nitrospira OTUs varied within the estuarine samples, showing a geographical pattern. Salinity and pH were the most important environmental drivers affecting the distribution of comammox Nitrospira in estuarine tidal flat wetlands. The abundance of comammox Nitrospira was further negatively correlated with high ammonia and nitrite concentrations. Altogether, this study revealed the existence, abundance and distribution of comammox Nitrospira and the driving environmental factors in estuarine ecosystems, thus providing insights into the ecological niches of this recently discovered nitrifying consortium and their contributions to nitrification in global estuarine environments.

Bacterial community colonization on tire microplastics in typical urban water environments and associated impacting factors

Only limited information is available on bacterial communities' dynamics on tire microplastics in urban water environments. This study exploited 16S rDNA high-throughput sequencing to characterize bacterial communities on tire microplastics, using three different tire brands and tire sizes, in two typical urban water environments, including an influent pond of constructed wetland (CW) and its subsequent effluent into a landscape river (LR) during three different periods, namely, 1 month, 3 and 6 months. Results showed that the abundance of bacterial colonization on tire microplastics will increase over time. Proteobacteria, Bacteroidetes were the dominant bacteria at a phylum level, although they exhibited dynamic changes. At a genus level, the identifiable bacteria found in tire microplastics was generally the common bacteria in wastewater discharge, such as Aquabacterium and Denitratisoma. Additionally, alpha diversity showed no significant differences in bacterial communities at the same locations. While beta diversity showed that the bacterial communities on the tire microplastics in the two locations was different. BugBase revealed that tire microplastics could support pathogenic bacteria in urban water environments. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) indicated that the abundance of microorganisms associated with metabolism and degradation increased with time. Moreover, the ambient environmental factors were the main influencing factors of bacterial communities on tire microplastics. Herein, the contribution rate of nutrient salts (NO₂-N, NO₃-N, NH₄-N, CODcr) was approximately 63%, and that of environmental physical factors of T and pH was 50%. While physicochemical factors, including particle size, contact angle, element content only had a slight impact. Accordingly, tire microplastics, as an emerging environmental pollutant, can act as carries for bacterial colonization and propagation, particularly harmful microorganisms. Therefore, the obtained findings can provide new insight into potential risks of harmful microorganisms that colonize tire microplastics in urban water environments.

Robust nitrate removal and bioenergy generation with elucidating functional microorganisms under carbon constraint in a novel multianode tidal constructed wetland coupled with microbial fuel cell

This study investigated synthetic wastewater treatment under low inflow C/N ratio and characterized NO₃^--N-transforming and electricity-producing bacteria in a multi-anode tidal constructed wetland-microbial fuel cell (TFCW-MFC). The optimal concurrent average removal rates of NH₄⁺-N and NO₃^--N were 73% and 78%, respectively, under a flood/rest/flood time of 4 h/2h/4h in "tide" mode accompanied by one recirculation. The lowest NO₃^--N concentration among all anodes was observed when the electrode gap was 45 cm. Similarly, the 45 cm anode exhibited selective enrichment of Variovorax and Azoarcus. Correction analysis showed that the high relative abundance of Azoarcus was crucial in enhancing NO₃^--N removal, and the internal resistance significantly decreased as the relative abundance of Acidovorax increased. These results suggest that NO₃^--N removal and bioelectricity generation can be promoted in a TFCW-MFC with limited carbon by improving the culture conditions for specific genera.

Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary

Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.

Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions

Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.

Spatial distribution of phthalate acid esters in sediments and its relationships with anthropogenic activities and environmental variables of the Jiaozhou Bay

The spatial distribution of phthalate acid esters (PAEs) in sediments of the Jiaozhou Bay and its relationships with anthropogenic activities and environmental variables were investigated in this work. Thirteen PAEs were prevalent in sediments and the total PAE concentrations ranged from 462.1 to 15,133.2 μg/kg. The PAE concentrations increased northeastward and northwestward from the bay mouth in saddle shapes and the highest concentrations were located in the northeastern region according to the spatial distribution patterns generated by geographic information systems. The rivers were the main routes for transporting pollutants into the bay and terrigenous PAEs diluted offshore, so the PAE distribution in sediments was originated from anthropogenic activity intensity. There were strong positive correlations among PAEs with each other, except for di-n-octyl phthalate, and the average residence time (ART) exerted a significant positive impact on the PAE concentrations by Pearson correlation and redundancy analysis. The dibutyl phthalate and di-(2-ethylhexyl) phthalate had high risks to organisms in the northeast and west regions according to the environmental risk limits and risk quotients. The results might provide new insights into the PAE researches and supply information for environmental management and remediation.

Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach

Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia-oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia-oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia-oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis-Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.

Diversity and abundance of comammox bacteria in the sediments of an urban lake

AIMS

Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia-oxidizing microbe exists in urban lakes and to determine the factors influencing its existence.

METHODS AND RESULTS

This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia-oxidizing micro-organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co-existed with ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43 × 10⁸ , 1·07 × 10⁸ , 3·24 × 10⁷ and 3·21 × 10¹¹ copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria.

CONCLUSIONS

Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.

Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils

Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC_1:5) and NH₄-N compared to irrigation with freshwater, while NO₃-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO₃⁻N, and pH, while AOB communities were only significantly associated with NO₃⁻N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.

Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas

Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments. Massive polyP granules were observed under confocal microscopy in samples from very low DIP environments. The composition of sponge symbiotic microbes was analyzed by high-throughput sequencing and the corresponding polyphosphate kinase (ppk) genes were detected. Sequence analysis revealed that in the low DIP environment, those sponges with higher polyP content and enrichment rates had relatively higher abundances of cyanobacteria. Mantel tests and canonical correspondence analysis (CCA) examined that the polyP enrichment rate was most strongly correlated with the structure of microbial communities, including genera Synechococcus, Rhodopirellula, Blastopirellula, and Rubripirellula. About 50% of ppk genes obtained from the total DNA of sponge holobionts, had above 80% amino acid sequence similarities to those sequences from Synechococcus. In general, it suggested that sponges employed differentiated strategies towards the use of phosphorus in different nutrient environments and the symbiotic Synechococcus could play a key role in accumulating polyP.

Nutrients and heavy metals mediate the distribution of microbial community in the marine sediments of the Bohai Sea, China

The Bohai Sea, one of the largest marginal seas in China, is extensively influenced by human and industrial activities. The pollutant loads from anthropogenic activities have induced severe ecological problems. The study investigates the physicochemical characteristics of seawater and sediments in Bohai Bay and Laizhou Bay of the Bohai Sea. The diversity and composition of microbial community in sediments are analyzed by 16S rRNA gene amplicon sequencing. The sequencing results present 16 phyla and 31 classes from the samples. Proteobacteria constituted a dominant phylum, of which the classes of Gamma-, Delta-, and Epsilon-are predominant sub-divisions. Nitrogen, phosphorus, and sulfur cycling related microbes present high abundance in both bays. The metabolism of organic matters is the main factor that influences the distribution of microbial communities in Bohai Bay, while the inflow of Yellow River is the dominant factor that influences the distribution of microbial communities in Laizhou Bay. Sulfur oxidizing process is expected to be positively influenced by heavy metals, while ammonia (NH₄⁺) oxidizing process is prone to be negatively affected by heavy metals in both bays. Microbial communities in the offshore sediments of Laizhou Bay and the majority microbial communities in Bohai Bay sediments are subject to similar predominant controlling factors. This phenomenon is likely ascribed to ocean circulation. The results of this study can provide constructive guidelines on ecosystem management of marginal seas in Bohai and elsewhere.

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.

Dynamics and environmental importance of anaerobic ammonium oxidation (anammox) bacteria in urban river networks

Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 10⁶ to 3.9 × 10⁷ copies g^-1 dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH₄⁺) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks.

The biological denitrification coupled with chemical reduction for groundwater nitrate remediation via using SCCMs as carbon source

Renewable additional carbon sources for groundwater denitrification, such as sustainable-releasing compound carbon source materials (SCCMs), are required. This work reports long-term groundwater denitrification with permeable reactive barriers filled with SCCMs; the coupling of biological denitrification and chemical reduction avoided the need for a continuous carbon source supply. Four 370-day lab-scale permeable reactive barrier experiments with four SCCMs showed that NO₃^- removal efficiency in zero-valent iron (ZVI) SCCMs was higher than in ZVI-free SCCMs. In the ZVI SCCMs, the NO₃^- removal reaction began quickly in the early stage, owing to ZVI chemical reduction, whereas biological denitrification was lower and incomplete with a NO₂^- concentration of 0.8 mg L^-1 in the ZVI SCCM system. As the chemical reduction efficiency decreased, the biological denitrification efficiency increased, and the highest NO₃^- removal efficiency was 98.8%. Decreasing the Fe²⁺concentration decreased ZVI chemical reduction. High-throughput sequencing indicated that the proportion of denitrifying bacteria attached to the SCCMs was up to 34.4% at the family level, leading to the denitrification gene being predominant. Quantitative PCR indicated increased microbial metabolic activity, richer bacterial community diversity, and more bacteria. Long-term monitoring data for SCCMs will help realize the use of biological denitrification coupled with chemical reduction for groundwater NO₃^- remediation.

An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake

Ammonium-oxidizing archaea (AOA) and bacteria (AOB) play crucial roles in ammonium oxidation in freshwater lake sediment. However, previous reports on the predominance of AOA and AOB in the surface sediment of Lake Taihu have been based on DNA levels, detecting the total abundance of microbiota (including inactive cells), and have resulted in numerous contradictory conclusions. Existing RNA-level studies detecting active transcription are very limited. The current study, using RNA-based real-time quantification and clone library analysis, demonstrated that the amoA gene abundance of active AOB was higher than that of active AOA, despite conflicting results at the DNA level. Further exploration revealed a significant positive correlation between the potential nitrification rate (PNR) and the abundance of AOA and AOB at the RNA level, with irregular or contradictory correlation found at the DNA level. Ultimately, using quantitative analysis of RNA levels, we show AOB to be the active dominant contributor to ammonium oxidation. Our investigations also indicated that AOB were more diverse in high-ammonium lake regions, with Nitrosomonas being the active and dominating cluster, but that AOA had an advantage in the low-ammonium lake regions.

Development of microbial community-based index of biotic integrity to evaluate the wetland ecosystem health in Suzhou, China

The development of microbial community-based biological indicators for assessing aquatic ecological status is urgently needed in heavily impaired regions, due to the local extinction of traditional indicator macro-organisms. The aim of this study was to develop and validate a microbial community-based index of biotic integrity (MC-IBI) to assess the health of wetlands in Suzhou, China. High-throughput sequencing was used to obtain information about microbial communities in wetlands and to investigate the health of the wetlands. When constructing the index, we selected what we considered were the most important environmental factors and biological parameters, and identified sensitive and tolerant species. We then used the index to evaluate the health of the inflows and outflows of 15 wetlands in Suzhou. The results showed that, of the 30 samples collected at the 10 impacted inflow sites, 2 were classified as "poor," 5 were "commonly," 18 were sub-healthy, and 5 were healthy; at the restored outflow sites, 24 were "healthy" and 6 were "sub-healthy." The health was worst at the inflows of wetlands that received agricultural effluent, followed by those that received industrial effluent, and was best at those that received urban effluent. The results from our study show that this newly developed MC-IBI gave reasonable evaluations of the health of wetland ecosystems. This application demonstrates that the evaluation system was feasible and we suggest that evaluations that further MC-IBI evaluation approaches should be developed further in the future.

The Characteristics and Dynamics of Cyanobacteria-Heterotrophic Bacteria Between Two Estuarine Reservoirs - Tropical Versus Sub-Tropical Regions

In this study, Illumina MiSeq sequencing technique was employed to explore the characteristics and dynamics of cyanobacteria–heterotrophic bacteria between two estuarine reservoirs in sub-tropical (reservoir A in Shanghai) and tropical (reservoir B in Singapore) regions. The results indicated that significant differences in bacterial community composition were found between two estuarine reservoirs, which influenced by varied environmental variables. The environmental heterogeneity in reservoir A was much higher, which indicated that the composition of bacterial community in reservoir A was more complex. In contrast, reservoir B provided a suitable and temperate water environment conditions for bacterial growth, which resulted in higher community diversity and less co-exclusion correlations. The molecular ecological network indicated that the presence of dominant bacterial community in each of the reservoir were significant different. These differences mainly reflected the responses of bacterial community to the variations of environmental variables. Although Synechococcus was the dominant cyanobacterial species in both reservoirs, it exhibited co-occurrence patterns with different heterotrophic bacteria between reservoirs. In addition, the cyanobacteria–heterotrophic bacteria interaction exhibited highly dynamic variations, which was affected by nutrition and survive space. Also, the co-occurrence of Microcystis and Pseudanabaena found in reservoir B implied that the non-N-fixing Microcystis accompanied with N-fixing Pseudanabeana occurrence in freshwater lakes, so as to better meet the demand for nitrogen source.

Sponge-microbe partnerships are stable under eutrophication pressure from mariculture

Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.

Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake

The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring–winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.

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.

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.

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems

Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.

Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination

The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment. The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.

Environmental Factors Shape Water Microbial Community Structure and Function in Shrimp Cultural Enclosure Ecosystems

The effects of environmental factors on water microbial communities have been extensively studied, but little is known about the effects in shrimp cultural enclosure ecosystems. We analyzed 16S rRNA gene amplicons to determine the principal environmental factors that shape the structure and function of microbial communities in shrimp cultural enclosure ecosystems from Guangdong and Hainan provinces, in China. High quality sequences were clustered into operational taxonomic units (OTUs) at the 97% similarity level, generating 659-1,835 OTUs per sample. The 10 most abundant phyla were Proteobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Firmicutes, Chlorobi, Chloroflexi, and Chlamydiae. The results of canonical correspondence analyses (CCA) indicated that salinity, total phosphate (TP), total nitrogen (TN), temperature, and pH were the most important factors shaping microbial community structure. Differences in microbial community structure between high and low salinity samples were explained by changes in the relative abundances of some OTUs (e.g., OTU5, OTU19, OTU21, OTU39, and OTU71). Moreover, the contribution of spatial distribution to the microbial community assembly was investigated via aggregated boosted tree (ABT) analyses, and the results indicated spatial isolation was not a major factor affecting the phylogenetic diversity and phylotypes of water microbial communities. Furthermore, we predicted water microbial community functional profiling using the PICRUSt program and principal component analyses (PCA) suggested that salinity was a major contributor to the structure and function of the microbial communities. Collectively, these results showed that environmental factors influenced the structure and function of water microbial communities, while salinity was the principal environmental factor instead of temperature, TP, TN, and pH in shrimp cultural enclosure ecosystems.

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes

Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd ₁-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.

Sediment bacterial communities in a eutrophic lake influenced by multiple inflow-rivers

Sediment bacterial communities are sensitive to environmental fluctuations, particularly external input sources. Studying the relationships between bacterial community distribution and the estuarine environment is critical for understanding the river-lake confluence ecosystem and the effect of inflow-rivers on lakes. In the present study, bacterial communities from the sediments of 14 estuaries and four pelagic sites of the Taihu Lake were investigated via high-throughput sequencing. The results demonstrated that Delta-, Beta-, and Gamma-proteobacteria, Acidobacteria, Nitrospira, Bacilli, Anaerolineae, and Actinobacteria were the major classes in sediment bacterial communities of the Taihu Lake. In general, the inflow-rivers of different pollution types have distinctly different influences on sediment bacterial communities of the lake. The bacterial community composition and physicochemical properties of pelagic sites were closer to those of the estuaries of western region which was polluted by serious industrial and agricultural pollution. The bacterial community diversity of estuaries was lower than those of pelagic sites. Spearman correlation analysis indicated that α-diversity of the bacterial community was significantly correlated with C/N, total nitrogen, and total carbon in estuarine sediments. Redundancy analysis revealed that the variance in bacterial community composition was also significantly associated with C/N (24.9%) followed by total phosphorus (15.8%), nitrite (7.2%), and nitrate (7.7%) among different estuaries. This study provides a reference to understand the influence of inflow-rivers on the lake ecosystem, which offered a basic guidance for maintaining the ecological system and protecting the water environment of lacustrine basin.

Effects of silver nanoparticles on nitrification and associated nitrous oxide production in aquatic environments

Silver nanoparticles (AgNPs) are the most common materials in nanotechnology-based consumer products globally. Because of the wide application of AgNPs, their potential environmental impact is currently a highly topical focus of concern. Nitrification is one of the processes in the nitrogen cycle most susceptible to AgNPs but the specific effects of AgNPs on nitrification in aquatic environments are not well understood. We report the influence of AgNPs on nitrification and associated nitrous oxide (N₂O) production in estuarine sediments. AgNPs inhibited nitrification rates, which decreased exponentially with increasing AgNP concentrations. The response of nitrifier N₂O production to AgNPs exhibited low-dose stimulation (<534, 1476, and 2473 μg liter^-1 for 10-, 30-, and 100-nm AgNPs, respectively) and high-dose inhibition (hormesis effect). Compared with controls, N₂O production could be enhanced by >100% at low doses of AgNPs. This result was confirmed by metatranscriptome studies showing up-regulation of nitric oxide reductase (norQ) gene expression in the low-dose treatment. Isotopomer analysis revealed that hydroxylamine oxidation was the main N₂O production pathway, and its contribution to N₂O emission was enhanced when exposed to low-dose AgNPs. This study highlights the molecular underpinnings of the effects of AgNPs on nitrification activity and demonstrates that the release of AgNPs into the environment should be controlled because they interfere with nitrifying communities and stimulate N₂O emission.

Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.

Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants

This study aimed to investigate the variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems without prechlorination and associated effects on the transformation of nitrogen pollutants by using a designed model pipe system. The results showed the transformation of nitrogen pollutants was obvious during the biofilm formation. The richness and diversity of the microbial communities changed significantly. The higher abundance of Nitrospirae in biofilm samples significantly contributed to biological nitrification. In particular, the stable content of Bacteroidetes in the biofilm and soluble microbial products released by the biomass might have enhanced the increase in dissolved organic nitrogen. In addition, the variation tendency of nitrogen functional gene abundances and their strong effects on NH₄⁺-N, NO₂^--N, and NO₃^--N transformation were clearly observed. These findings provide new insights into the evolution of microbial communities and functional genes during the initial operation period of real-world raw water distribution pipes and highlight management and possible safety issues in the subsequent water treatment process.