Molecular detection of Candidatus Scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea, China

Nitrogen Removal Performance and Microbial Community Structure of IMTA Ponds (Apostistius japonicus-Penaeus japonicus-Ulva)

Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

The swimming crab, Portunus trituberculatus, is one of the main aquaculture species in Chinese coastal regions due to its palatability and high economic value. To obtain a better understanding of the genetic diversity of P. trituberculatus in the Bohai Sea, the present study used 40 SSR loci to investigate the genetic diversity and population structure of 420 P. trituberculatus individuals collected from seven populations in the Bohai Sea. Genetic parameters revealed a low level of genetic diversity in the cultured population (SI = 1.374, He = 0.687, and PIC = 0.643) in comparison with wild populations (SI ≥ 1.399, He ≥ 0.692, and PIC ≥ 0.651). The genetic differentiation index (Fst) and gene flow (Nm) ranged from 0.001 to 0.060 (mean: 0.022) and 3.917 to 249.750 (mean: 31.289) respectively, showing a low differentiation among the seven populations of P. trituberculatus. Population structure analysis, phylogenetic tree, and principal component analysis (PCA) demonstrated that the seven groups of P. trituberculatus were divided into four subpopulations (K = 4), but the correlation between genetic structure and geographical distribution was not obvious. These results are expected to provide useful information for the fishery management of wild swimming crabs.

Insights into nitrogen removal and microbial response of marine anammox bacteria-based consortia treating saline wastewater: From high to moderate and low salinities

Marine anammox bacteria (MAB) have promising nitrogen removal performance in high saline wastewater treatment. Nevertheless, the impact resulting from moderate and low salinities on MAB is still unclear. Herein, MAB were applied to treat saline wastewater from high to moderate and low salinities for the first time. Independent of salinities (35-3.5 g/L), MAB consistently exhibited good nitrogen removal performance, and maximum total nitrogen removal rate (0.97 kg/(m³·d)) occurred at 10.5 g/L salts. More extracellular polymeric substances (EPSs) were secreted by MAB-based consortia to resist hypotonic surroundings. However, a sharp EPS decrease was accompanied by the collapse of MAB-driven anammox process, and MAB granules disintegrated due to long-term exposure to salt-free environment. The relative abundance of MAB varied from 10.7% to 15.9% and 3.8% as salinity decreased from 35 to 10.5 and 0 g/L salts. These findings will provide practical implementation of MAB-driven anammox process treating wastewater with different salinities.

A critical review on microbial ecology in the novel biological nitrogen removal process: Dynamic balance of complex functional microbes for nitrogen removal

The novel biological nitrogen removal process has been extensively studied for its high nitrogen removal efficiency, energy efficiency, and greenness. A successful novel biological nitrogen removal process has a stable microecological equilibrium and benign interactions between the various functional bacteria. However, changes in the external environment can easily disrupt the dynamic balance of the microecology and affect the activity of functional bacteria in the novel biological nitrogen removal process. Therefore, this review focuses on the microecology in existing the novel biological nitrogen removal process, including the growth characteristics of functional microorganisms and their interactions, together with the effects of different influencing factors on the evolution of microbial communities. This provides ideas for achieving a stable dynamic balance of the microecology in a novel biological nitrogen removal process. Furthermore, to investigate deeply the mechanisms of microbial interactions in novel biological nitrogen removal process, this review also focuses on the influence of quorum sensing (QS) systems on nitrogen removal microbes, regulated by which bacteria secrete acyl homoserine lactones (AHLs) as signaling molecules to regulate microbial ecology in the novel biological nitrogen removal process. However, the mechanisms of action of AHLs on the regulation of functional bacteria have not been fully determined and the composition of QS system circuits requires further investigation. Meanwhile, it is necessary to further apply molecular analysis techniques and the theory of systems ecology in the future to enhance the exploration of microbial species and ecological niches, providing a deeper scientific basis for the development of a novel biological nitrogen removal process.

Bacterial taxonomic and functional profiles from Bohai Sea to northern Yellow Sea

Microbial distribution patterns are the result of a combination of biotic and abiotic factors, which are the core issues in microbial ecology research. To better understand the biogeographic pattern of bacteria in water environments from the Bohai Sea to the northern Yellow Sea, the effects of environmental factors, and spatial distance on the structure of bacterial communities in marine water were investigated using high-throughput sequencing technology based on 16S rRNA genes. The results showed that Proteobacteria, Bacteroidetes, Actinobacteri, Desulfobacterota, and Bdellovibrionota were the dominant phyla in the study area. A clear spatial pattern in the bacterial community was observed, and environmental factors, including salinity, nutrient concentration, carbon content, total phosphorus, dissolved oxygen, and seawater turbidity emerged as the central environmental factors regulating the variation in bacterial communities. In addition, the study provides direct evidence of the existence of dispersal limitation in this strongly connected marine ecological system. Therefore, these results revealed that the variation in bacterial community characteristics was attributed to environmental selection, accompanied by the regulation of stochastic diffusion. The network analysis demonstrated a nonrandom co-occurrence pattern in the microbial communities with distinct spatial distribution characteristics. It is implied that the biogeography patterns of bacterial community may also be associated with the characteristics of co-occurrence characterize among bacterial species. Furthermore, the PICRUSt analysis indicated a clear spatial distribution of functional characteristics in bacterial communities. This functional variation was significantly modulated by the environmental characteristics of seawater but uncoupled from the taxonomic characteristics of bacterial communities (e.g., diversity characteristics, community structure, and co-occurrence relationships). Together, this findings represent a significant advance in linking seawater to the mechanisms underlying bacterial biogeographic patterns and community assembly, co-occurrence patterns, and ecological functions, providing new insights for identifying the microbial ecology as well as the biogeochemical cycle in the marine environment.

Anammox bacteria drive fixed nitrogen loss in hadal trench sediments

Benthic N₂ production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N₂ production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N₂ production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N₂ production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis.

Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua

The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.

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.

Nitrogen-cycling gene pool shrunk by species interactions among denser bacterial and archaeal community stimulated by excess organic matter and total nitrogen in a eutrophic bay

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH₃-N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

Environmental filtering dominates bacterioplankton community assembly in a highly urbanized estuarine ecosystem

Estuaries are important in terms of biodiversity, biogeochemical function, and ecological balance due to their intense land-sea interactions. The sustainability of estuarine ecosystem function relies on a good understanding of the ecological processes related to microbial communities. However, microbial community assembly in such ecosystems is still not well understood. Here, based on 16S rRNA sequencing, we investigated the bacterioplankton community structure in the Pearl River Estuarine system during the wet and dry seasons. Results showed that there were significant seasonal and spatial variations in the bacterioplankton communities of the estuary, with seasonal variations being more remarkable. Multiple bacterioplankton with different abundances in the wet and dry seasons were observed, e.g., the class Actinobacteria and Oxyphotobacteria were enriched in the wet season, whereas Alphaproteobacteria and Saccharimonadia were more abundant in the dry season. Both variation partitioning and null model analysis revealed that environmental filtering dominated the bacterioplankton community assembly in the Pearl River Estuary. Water physical properties (e.g., salinity and temperature), nutrient content (e.g., nitrate), and upstream land use (e.g., urban land cover) together determined the distribution of the bacterioplankton composition in this highly urbanized estuarine ecosystem. These findings would help improve our understanding of the bacterioplankton communities in estuarine ecosystems and provide a theoretical foundation for estuarine ecological health management.

Influence of environmental factors on benthic nitrogen fixation and role of sulfur reducing diazotrophs in a eutrophic tropical estuary

Benthic nitrogen fixation in the tropical estuaries plays a major role in marine nitrogen cycle, its contribution to nitrogen budget and players behind process is not well understood. The present study was estimated the benthic nitrogen fixation rate in a tropical estuary (Cochin) and also evaluated the contribution of various diazotrophic bacterial communities. Nitrogen fixation was detected throughout year (0.1-1.11 nmol N g^-1 h^-1); higher activity was observed in post-monsoon. The nifH gene abundance was varied from 0.8 × 10⁴ to 0.6 × 10⁸ copies g^-1dry sediment; highest was detected in post-monsoon. The Cluster I and Cluster III were the dominant diazotrophs. Sulfur reducing bacterial phylotypes (Deltaproteobacteria) contributed up to 2-72% of total nitrogen fixation. These bacteria may provide new nitrogen to these systems, counteracting nitrogen loss via denitrification and anammox. Overall, the study explained the importance of benthic nitrogen fixation and role of diazotrophs in a monsoon influenced tropical estuarine environments.

Geochemical transition zone powering microbial growth in subsurface sediments

No other environment hosts as many microbial cells as the marine sedimentary biosphere. While the majority of these cells are expected to be alive, they are speculated to be persisting in a state of maintenance without net growth due to extreme starvation. Here, we report evidence for in situ growth of anaerobic ammonium-oxidizing (anammox) bacteria in ∼80,000-y-old subsurface sediments from the Arctic Mid-Ocean Ridge. The growth is confined to the nitrate-ammonium transition zone (NATZ), a widespread geochemical transition zone where most of the upward ammonium flux from deep anoxic sediments is being consumed. In this zone the anammox bacteria abundances, assessed by quantification of marker genes, consistently displayed a four order of magnitude increase relative to adjacent layers in four cores. This subsurface cell increase coincides with a markedly higher power supply driven mainly by intensified anammox reaction rates, thereby providing a quantitative link between microbial proliferation and energy availability. The reconstructed draft genome of the dominant anammox bacterium showed an index of replication (iRep) of 1.32, suggesting that 32% of this population was actively replicating. The genome belongs to a Scalindua species which we name Candidatus Scalindua sediminis, so far exclusively found in marine sediments. It has the capacity to utilize urea and cyanate and a mixotrophic lifestyle. Our results demonstrate that specific microbial groups are not only able to survive unfavorable conditions over geological timescales, but can proliferate in situ when encountering ideal conditions with significant consequences for biogeochemical nitrogen cycling.

Investigation of nitrogen pollutants transformation and its pathways along the long-distance prechlorinated raw water distribution system

Understanding the transformation pattern of nitrogen (N) pollutants and its pathways in the prechlorinated raw water distribution system (PRWDS) is vital for controlling the stablitiy and safety of raw water qulity. This study investigated the N transformation, N functional genes and their correlations to find the N transformation pathways along the PRWDS. Results suggested that simultaneous nitrification, anaerobic ammonium oxidation and denitrification (SNAD) contribute to the N transformationin the PRWDS. Along the pipeline, anammox 16S rRNA (9.18 × 10⁷-8.41 × 10⁸ copies/g), limited by prechlorination, was the most abundant N functional genes and anammox process was the main pathway of ammonia nitrogen (NH₄⁺-N). The decreasing NH₄⁺-N was connected with Planctomycetes, Nitrospira and abundance of nxrA attributing to the joint effort of anammox and declined nitrification. The concentration of nitrate (NO₃^--N) increasing at first and then decreasing, was correlated positively with Sphingomonas. because of the declined nitritication and increased denitrification. Besides, the NO₃^--N→NO₂^--N process was considered to be primary NO₃^--N transformation pathways. Increases in the concentration of dissolved organic nitrogen (DON) and nitrite (NO₂^--N) observed in the PRWDS had positive correlation with relative abundance of Pseudomonas. We believe that prechlorination shaped the particular bacterialcharacteristics in biofilms and influenced the N transformation pathways indirectly, resulting in the varying N transformation rules in PRWDSs. Moreover, systematic and extended research is particularly vital for determining the effects of changes in source water quality and environmental conditions on bacterial community structure and N conversion along PRWDSs.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

Anaerobic ammonia-oxidizing bacteria in tropical bioaugmented zero water exchange aquaculture ponds

Bioaugmented zero water exchange aquaculture production systems (ZWEAPS) maintained with minimal or no water exchange prevent the ammonia accumulation in the system, leading to environmental sustainability and biosecurity. The microbes in the bioaugmented ZWEAPS plays a major role in maintaining low levels of ammonia through ammonia oxidation and nitrite oxidation. The comprehensive understanding on anammox population in the systems will provide an insight on the environmental factors controlling the functional anammox bacterial communities for potential biostimulation and augmented ammonia removal in ZWEAPS. The sediment metagenome of such three tropical bioaugmented ZWE shrimp culture ponds were analysed to determine the diversity, distribution and abundance of anaerobic ammonia-oxidizing (anammox) bacteria based on hydrazine oxidoreductase (hzo) gene as a phylogenetic marker. The restriction fragment length polymorphism (RFLP) phylotypes from the clone libraries were identified with maximum distribution to Candidatus Kuenenia, as the dominant population in the study sites with high ammonia load followed by Candidatus Scalindua. The environmental factors associated with the abundance and diversity of the anammox population were analysed using RDA and Pearson correlation. The samples of final culturing period (75th day) of TCR-S ZWE pond was observed with the highest operational taxonomic unit (OTU)-based diversity, where comparatively higher ammonia (water 0.71 mg L^-1 and sediment 1.21 mg L^-1) was recorded among the study sites. The gene abundance of the anammox population ranged from 10⁶ to 10⁷ copies per gram of sediment, in spite of less diversity. The physiochemical factors such as ammonia, nitrite, redox potential and the total organic carbon indicated a strong and positive correlation to the abundance and distribution of the anammox population, which highlights the importance of anammox communities and the potential of biostimulation for ammonia removal in the aquaculture systems.

Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone

To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.

Nitrogen release and its influence on anammox bacteria during the decay of Potamogeton crispus with different values of initial debris biomass

Aquatic macrophytes play a significant role in the nutrient cycle of freshwater ecosystems. However, nutrients from plant debris release into both sediments and overlying water if not timely harvested. To date, minimal information is available regarding nutrient release and its subsequent influences on bacterial communities with decaying debris. In this study, Potamogeton crispus was used as a model plant. Debris biomass levels of 0 g (control, J-CK), 10 g dry weight (DW) (100 g DW/m², J-10 g), 40 g DW (400 g DW/m2, J-40 g) and 80 g DW (800 g DW/m², J-80 g) were used to simulate the different biomass densities of P. crispus in field. The physicochemical parameters of overlying water and sediment samples were analysed. The community composition of anammox bacteria in the sediment was also analysed using 16S rRNA genes as markers. The results showed that dissolved oxygen and pH dramatically decreased, whereas total nitrogen (TN) and NH₄⁺-N concentrations increased in the overlying water in the initial stage of P. crispus decomposition. However, NO₃^--N concentration changes in the overlying water were more complicated. The concentrations of organic matter, TN and NH₄⁺-N in the sediment all increased, but the rate of increase varied among the groups with different initial biomass levels, indicating that these physicochemical properties in sediment are significantly affected by debris biomass level and decay time. In addition, the order of anammox bacteria abundance was J-40 g > J-CK > J-80 g > J-10 g. Moreover, the community structure of anammox bacteria were simpler compared to that of J-CK as debris biomass level increased. The results demonstrate that P. crispus debris decomposition could affect the ecological distribution of anammox bacteria. Such influence clearly varies with varying amounts of P. crispus biomass debris. This information could be useful for the management of aquatic macrophytes in freshwater ecosystems.

Shifts in the anammox bacterial community structure and abundance in sediments from the Changjiang Estuary and its adjacent area

Anaerobic ammonium oxidation (anammox) is an important process in marine nitrogen cycle. In this study, diverse anammox bacteria were identified in the sediments of the Changjiang (Yangtze) Estuary and its adjacent area. Specifically, the community characters of anammox bacteria in the studied area were studied by quantitative polymerase chain reaction (qPCR), as well as 16S rRNA gene- and functional gene (hzo)-based Roche 454 sequencing. The abundance of denitrifying bacteria detected by the nirS gene was greater than that of anammox bacteria. 16S rRNA and hzo gene fragments affiliating with known anammox bacterial lineages were recovered, and the two major phylotypes belonged to the Candidatus Scalindua (Ca. Scalindua) genus, with >90% sequence similarity. A phylogenetic analysis detected the Scalindua and Brocadia genera together with some anammox-like bacterial clusters, which suggested a higher diversity in the studied ecosystem than in open ocean environment, where only Scalindua genus was detected. A redundancy analysis (RDA) showed that total organic carbon (TOC) and total nitrogen (TN) content in sediments significantly influenced anammox bacterial abundance of. Spearman correlation analyses confirmed that the spatial variation in anammox bacterial abundance was highly correlated with TOC (P<0.01) and TN (P<0.01) contents in sediments.

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.

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.

Effects of Salts on the Activity and Growth of "Candidatus Scalindua sp.", a Marine Anammox Bacterium

Four salts, SEALIFE (a synthetic sea salt), NaCl, Na2SO4, and NaCl+KCl, were applied to monitor the effects of salinity on "Candidatus Scalindua sp.", a marine anaerobic ammonium oxidation (anammox) bacterium. The highest ammonium consumption of 10 μmol mg protein-1 d-1 was observed at 88 mmol L-1 of Na in the presence of NaCl. The highest inorganic carbon uptake of 0.6 μmol mg protein-1 d-1 was observed at 117 mmol L-1 of Na and at 16 mmol L-1 of K in the presence of NaCl+KCl. Thus, Na and K are both important for maintaining a high growth rate of "Candidatus Scalindua sp."

Anaerobic Ammonium Oxidation in Acidic Red Soils

Anaerobic ammonium oxidation (anammox) has been proven to be an important nitrogen removal process in terrestrial ecosystems, particularly paddy soils. However, the contribution of anammox in acidic red soils to nitrogen loss has not been well-documented to date. Here, we investigated the activity, abundance, and distribution of anammox bacteria in red soils collected from nine provinces of Southern China. High-throughput sequencing analysis showed that Candidatus Brocadia dominates the anammox bacterial community (93.03% of sequence reads). Quantification of the hydrazine synthase gene (hzsB) and anammox 16S rRNA gene indicated that the abundance of anammox bacteria ranged from 6.20 × 10⁶ to 1.81 × 10⁹ and 4.81 × 10⁶ to 4.54 × 10⁸ copies per gram of dry weight, respectively. Contributions to nitrogen removal by anammox were measured by a ¹⁵N isotope-pairing assay. Anammox rates in red soil ranged from 0.01 to 0.59 nmol N g⁻¹ h⁻¹, contributing 16.67–53.27% to N₂ production in the studied area, and the total amount of removed nitrogen by anammox was estimated at 2.33 Tg N per year in the natural red soils of southern China. Pearson correlation analyses revealed that the distribution of anammox bacteria significantly correlated with the concentration of nitrate and pH, whereas the abundance and activity of anammox bacteria were significantly influenced by the nitrate and total nitrogen concentrations. Our findings demonstrate that Candidatus Brocadia dominates anammox bacterial communities in acidic red soils and plays an important role in nitrogen loss of the red soil in Southern China.

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples

Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH₄⁺ and NO₂^- biochemically to form N₂ gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.

Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea

The eutrophic Bohai Sea receives large amount of suspended material, nutrients and contaminant from terrestrial runoff, and exchanges waters with the northern Yellow Sea through a narrow strait. This coastal region provides an ideal model system to study microbial biogeography. We performed high-throughput sequencing to investigate the distribution of bacterial taxa along spatial and environmental gradients. The results showed bacterial communities presented remarkable horizontal and vertical distribution under coastal gradients of spatial and environmental factors. Fourteen abundant taxa clustered the samples into three distinctive groups, reflecting typical habitats in shallow coastal water (seafloor depth ≤ 20 m), sunlit surface layer (at water surface with seafloor depth >20 m) and bottom water (at 2-3 m above sediment with seafloor depth >20 m). The most significant taxa of each cluster were determined by the least discriminant analysis effect size, and strongly correlated with spatial and environmental variables. Environmental factors (especially turbidity and nitrite) exhibited significant influences on bacterial beta-diversity in surface water (at 0 m sampling depth), while community similarity in bottom water (at 2-3 m above sediment) was mainly determined by depth. In both surface and bottom water, we found bacterial community similarity and the number of OTUs shared between every two sites decreased with increasing geographic distance. Bacterial dispersal was also affected by phosphate, which was possible due to the high ratios of IN/IP in this coastal sea area.

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.

Effects of various fertilization regimes on abundance and activity of anaerobic ammonium oxidation bacteria in rice-wheat cropping systems in China

Anaerobic ammonium oxidation (anammox) is an important process in many marine and paddy ecosystems. However, few studies have reported on the contribution to the nitrogen cycle of anammox and its dynamics in rice-wheat cropping systems with different fertilization regimes. Here, isotope tracing and molecular techniques were used to determine the potential rates of anammox and their association with bacterial abundance, diversity, and activity. Rice-wheat cropping systems at two sites in Jiangsu Province, China were selected and the treatments at each site were: 1) no fertilization (CK), 2) 100% chemical fertilization (CF), 3) pig manure compost plus 50% chemical fertilization (PMCF), and 4) straw plus 100% chemical fertilization (SRCF). The results revealed that anammox bacteria with high abundance were detected in both the wheat and rice seasons. The abundance of anammox in PMCF treatment was higher than that in SRCF treatment in both Changshu and Jintan. Moreover, the abundance of anammox bacteria in CF treatment was significantly higher than that in CK in Changshu. Analysis of anammox hydrazine synthase β subunit (hzs-β) gene sequences showed that in the rice season, the anammox bacteria Ca. Brocadia, Ca. Scalindua, and Ca. Jettenia were present. In contrast, all of the anammox hydrazine oxidase (hzo) genes were affiliated with Ca. Brocadia, suggesting that hzs genes are more representative of anammox biological diversity compared to hzo. Sequences from the PMCF treatment where affiliated with both Ca. Jettenia and Ca. Brocadia, and showed the highest diversity. Anammox activity was detected in both the wheat and rice seasons, but there were significant differences between seasons. The anammox rates were in the range 0.34 to 1.04nmol dinitrogen gas∙g^-1 dry soil∙h^-1, and 3.15 to 9.62% of dinitrogen gas emissions were attributed to anammox. However, no significant difference among the fertilizer treatments for anammox activity was found in the study.

Genetic diversity of marine anaerobic ammonium-oxidizing bacteria as revealed by genomic and proteomic analyses of 'Candidatus Scalindua japonica'

Anaerobic ammonium-oxidizing (anammox) bacteria affiliated with the genus 'Candidatus Scalindua' are responsible for significant nitrogen loss in oceans, and thus their ecophysiology is of great interest. Here, we enriched a marine anammox bacterium, 'Ca. S. japonica' from a Hiroshima bay sediment in Japan, and comparative genomic and proteomic analyses of 'Ca. S. japonica' were conducted. Sequence of the 4.81-Mb genome containing 4019 coding regions of genes (CDSs) composed of 47 contigs was determined. In the proteome, 1762 out of 4019 CDSs in the 'Ca. S. japonica' genome were detected. Based on the genomic and proteomic data, the core anammox process and carbon fixation of 'Ca. S. japonica' were further investigated. Additionally, the present study provides the first detailed insights into the genetic background responsible for iron acquisition and menaquinone biosynthesis in anammox bacterial cells. Comparative analysis of the 'Ca. Scalindua' genomes revealed that the 1502 genes found in the 'Ca. S. japonica' genome were not present in the 'Ca. S. profunda' and 'Ca. S. rubra' genomes, showing a high genomic diversity. This result may reflect a high phylogenetic diversity of the genus 'Ca. Scalindua'.

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.

Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment

The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N₂, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.

Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes

Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas

Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater SiO32−-Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche differentiation between the shallow-water and deep-water sediment diazotrophic communities and suggests that the in situ physical and geochemical conditions play a more important role than geographical contiguity in determining the community similarity of the diazotrophic microbiota in marginal sea sediments.

Impact of extreme metal contamination at the supra-individual level in a contaminated bay ecosystem

Anthropogenic stressors impact the global environment and adversely affect the health of organisms and humans. This study was designed as an attempt to evaluate the ecological consequences of severe metal contamination at the supra-individual level based on a field investigation in Jinzhou Bay (JZB), North China in 2010. The chemical results showed high concentrations of metals in the sediment of JZB that were ~129 times greater than the local geochemical background. Furthermore, the measured metals exhibited considerably high toxicity potential indicated by sediment quality guidelines (SQGs). The mean SQGs quotients suggested the overall toxicity incidence was >70% in locations neighboring the Wulihe River mouth. Biomonitoring revealed 116 individuals distributed among a mere 6 species, 4 of which were polychaetes, at 33% of the sampling sites. Thus, few benthic organisms were present in the damaged community structures across the region, which was consistent with the extreme metal contamination. Moreover, the sediment quality assessment, in a weight of evidence framework, demonstrated that the sediment throughout the entire JZB was moderately to severely impaired, especially in the vicinity of the Wulihe River mouth. By synthesizing the present and previous chemical-biological monitoring campaigns, a possible cause-effect relationship between chemical stressors and benthic receptors was established. We also found that the hydrodynamics, sediment sources, and geochemical characteristics of the metals (in addition to the sources of the metals) were responsible for the geochemical distribution of metals in JZB. The significance of the overall finding is that the deleterious responses observed at the community level may possibly be linked to the extreme chemical stress in the sediment of JZB.

Impacts of human activities on distribution of sulfate-reducing prokaryotes and antibiotic resistance genes in marine coastal sediments of Hong Kong

Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments (P-value < 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment.

Diversity, Community Composition and Abundance of Anammox Bacteria in Sediments of the North Marginal Seas of China

Over the past few decades, anammox bacteria have been recognized as key players that contribute significantly to the release of large amounts of nitrogen in the global marine nitrogen cycle. In the present study, the diversity, community composition, and abundance of anammox bacteria from the sediments of four diverse regions in the north marginal seas in China were determined via clone library construction and a quantitative PCR analysis. The clone libraries retrieved by the 16S rRNA gene and Hzo gene markers indicated that “Candidatus Scalindua” was the predominant group throughout the sites examined. The 16S rRNA gene clone libraries revealed exceptional diversity by identifying two potential novel anammox clades, as evidenced by the high sequence similarities between these two clades and known anammox genera, and their unique phylogenetic positions with high bootstrap values. However, their potential roles in the anammox reaction need to be validated. Six novel members of Planctomycetes, divergent from the known genera of anammox bacteria, were also detected. A phylogenetic analysis by Hzo protein sequences revealed the existence of two known genera, i.e., “Candidatus Jettenia” and “Candidatus Anammoxoglobus”, which are rarely captured from marine sediments. Among all ecological parameters investigated, the distribution patterns and composition of anammox bacteria were found to be influenced by salinity, total organic matter, and temperature. The abundance of the anammox bacterial 16S rRNA gene from the sites examined ranged between 3.95×10⁵ and 9.21×10⁵ copies g⁻¹ wet sediment and positively correlated with the median size of the sediment sample.

Spatial-Temporal Changes of Bacterioplankton Community along an Exhorheic River

To date, few aquatic microbial ecology studies have discussed the variability of the microbial community in exorheic river ecosystems on both the spatial and seasonal scales. In this study, we examined the spatio-temporal variation of bacterioplankton community composition in an anthropogenically influenced exorheic river, the Haihe River in Tianjin, China, using pyrosequencing analysis of 16S rRNA genes. It was verified by one-way ANOVA that the spatial variability of the bacterioplankton community composition over the whole river was stronger than the seasonal variation. Salinity was a major factor leading to spatial differentiation of the microbial community structure into riverine and estuarial parts. A high temperature influence on the seasonal bacterial community variation was only apparent within certain kinds of environments (e.g., the riverine part). Bacterial community richness and diversity both exhibited significant spatial changes, and their seasonal variations were completely different in the two environments studied here. Furthermore, riverine bacterial community assemblages were subdivided into urban and rural groups due to changes in the nutritional state of the river. In addition, the nutrient-loving group including Limnohabitans, Hydrogenophaga, and Polynucleobacter were abundant in the urbanized Haihe River, indicating the environmental factors in these anthropogenic waterbodies heavily influence the core freshwater community composition.

Bioassessment of marine sediment quality using meiofaunal assemblages in a semi-enclosed bay

In order to assess marine sediment quality of a semi-enclosed bay, sediment and meiofaunal samples were analyzed at 35 stations in coastal waters of Bohai Bay, China. Concentrations of heavy metals (Cd, Cr, Cu, Ni, Pb, Zn, Co and Mn) in sediment were measured and the Hakanson potential ecological risk index coupled with the ratio of nematodes to copepods (N/C ratio) was used. Results showed that the concentration of Mn was the highest while Cd was the main risk contributor. The Hakanson potential ecological risk index indicated that all pollutants posed low risks in the study area. However, the N/C ratio exhibited different results compared with Hakanson potential ecological risk index. BIOENV analysis identified the concentration of Ni and sediment grain size as the most important environmental variables influencing meiofaunal assemblages. The present study indicated that, in marine sediment quality assessments, meiofaunal assemblages should be involved besides pollutant concentrations.

Bacterial and archaeal communities in sediments of the north Chinese marginal seas

Microbial communities of the Chinese marginal seas have rarely been reported. Here, bacterial and archaeal community structures and abundance in the surface sediment of four sea areas including the Bohai Sea (BS), North Yellow Sea (NYS), South Yellow Sea (SYS), and the north East China Sea (NECS) were surveyed by 16S ribosomal RNA (rRNA) gene pyrosequencing and quantitative PCR. The results showed that microbial communities of the four geographic areas were distinct from each other at the operational taxonomic unit (OTU) level, whereas the microbial communities of the BS, NYS, and SYS were more similar to each other than to the NECS at higher taxonomic levels. Across all samples, Bacteria were numerically dominant relative to Archaea, and among them, Gammaproteobacteria and Euryarchaeota were predominant in the BS, NYS, and SYS, while Deltaproteobacteria and Thaumarchaeota were prevalent in the NECS. The most abundant bacterial genera were putative sulfur oxidizer and sulfate reducer, suggesting that sulfur cycle processes might prevail in these areas, and the high abundance of dsrB (10(7)-10(8) copies g(-1)) in all sites verified the dominance of sulfate reducer in the north Chinese marginal seas. The differences in sediment sources among the sampling areas were potential explanations for the observed microbial community variations. Furthermore, temperature and dissolved oxygen of bottom water were significant environmental factors in determining both bacterial and archaeal communities, whereas chlorophyll a in sediment was significant only in structuring archaeal community. This study presented an outline of benthic microbial communities and provided insights into understanding the biogeochemical cycles in sediments of the north Chinese marginal seas.

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N₂ gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.

Diversity and distribution of planktonic anaerobic ammonium-oxidizing bacteria in the Dongjiang River, China

Anaerobic ammonium-oxidizing (anammox) process has recently been recognized as an important pathway for removing fixed nitrogen (N) from aquatic ecosystems. Anammox organisms are widely distributed in freshwater environments. However, little is known about their presence in the water column of riverine ecosystems. Here, the existence of a diverse anammox community was revealed in the water column of the Dongjiang River by analyzing 16S rRNA and hydrazine oxidation (hzo) genes of anammox bacteria. Phylogenetic analyses of hzo genes showed that Candidatus Jettenia related clades of anammox bacteria were dominant in the river, suggesting the ecological microniche distinction from freshwater/estuary and marine anammox bacteria with Ca. Brocadia and Kuenenia genera mainly detected in freshwater/estuary ecosystems, and Ca. Scalindua genus mainly detected in marine ecosystems. The abundance and diversity of anammox bacteria along the river were both significantly correlated with concentrations of NH4(+)-N based on Pearson and partial correlation analyses. Redundancy analyses showed the contents of NH4(+)-N, NO3(-)-N and the ratio of NH4(+)-N to NO2(-)-N significantly influenced the spatial distributions of anammox bacteria in the water column of the Dongjiang River. These results expanded our understanding of the distribution and potential roles of anammox bacteria in the water column of the river ecosystem.

Impact of volcanic ash on anammox communities in deep sea sediments

Subaerial explosive volcanism contributes substantial amounts of material to the oceans, but little is known about the impact of volcanic ash on sedimentary microbial activity. We have studied anammox communities in deep sea sediments near the volcanically active island of Montserrat, Lesser Antilles. The rates of anammox and denitrification in the sediments were measured using (15)N isotope pairing incubation experiments, while 16S rRNA genes were used to examine anammox community structures. The higher anammox rates were measured in sediment containing the lower accumulation of volcanic ash in the surface sediments, while the lowest activities were found in sediments with the highest ash deposit. 16S rRNA gene analysis revealed the presence of 'Candidatus Scalindua spp.' in the sediments. The lowest diversity of anammox bacteria was observed in the sediments with the highest ash deposit. Overall, this study demonstrates that the deposition of volcanic material in deep sea sediments has negative impacts on activity and diversity of the anammox community. Since anammox may account for up to 79% of N2 production in marine ecosystems, periods of extensive explosive volcanism in Earth history may have had a hitherto unrecognized negative impact on the sedimentary nitrogen removal processes.

Shotgun metagenomic data reveals significant abundance but low diversity of "Candidatus Scalindua" marine anammox bacteria in the Arabian Sea oxygen minimum zone

Anaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to “Candidatus Scalindua” species. Recently the genome assembly of a marine anammox enrichment culture dominated by “Candidatus Scalindua profunda” became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones (OMZs). Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the OMZ in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of “Candidatus Scalindua profunda” served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV) analysis was performed to assess diversity of the “Candidatus Scalindua” populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA) and hydrazine dehydrogenase (scal_03295, hdh), while other genes involved in anammox metabolism (narGH, nirS, amtB, focA, and ACS) had a lower coverage but could still be assembled and analyzed. The results show that “Candidatus Scalindua” is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low.

Diversity and spatial distribution of hydrazine oxidoreductase (hzo) gene in the oxygen minimum zone off Costa Rica

Anaerobic ammonia oxidation (anammox) as an important nitrogen loss pathway has been reported in marine oxygen minimum zones (OMZs), but the community composition and spatial distribution of anammox bacteria in the eastern tropical North Pacific (ETNP) OMZ are poorly determined. In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2. The anammox communities revealed by hzo genes and proteins in CRD-OMZ showed a low diversity. Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration. Nitrite and oxygen concentrations may therefore colimit the distribution of anammox bacteria in this area. Furthermore, transcriptional activity of anammox bacteria was confirmed by obtaining abundant hzo mRNA transcripts through qRT-PCR. A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment. Our study demonstrated that both cluster 1 and 2 anammox bacteria play an active role in the CRD-OMZ, and the cluster 1 abundance and transcriptional activity were higher than cluster 2 in both free-living and particle-attached fractions at both gene and transcriptional levels.