Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling.

The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use 15N and 18O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of 45N2O to 46N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual 15N-18O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.

Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.

Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean.

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013 to ∼2 × 1013 mol of C per year globally through the flux of ∼1 × 1014 to ∼2 × 1014 mol of N per year of the two steps of oxidation throughout the dark ocean.

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.

Population dynamics of methanogens and methanotrophs along the salinity gradient in Pearl River Estuary: implications for methane metabolism.

Methane, a major greenhouse gas, plays an important role in global carbon cycling and climate change. Methanogenesis is identified as an important process for methane formation in estuarine sediments. However, the metabolism of methane in the water columns of estuaries is not well understood. The goal of this research was to examine the dynamics in abundance and community composition of methanogens and methanotrophs, and to examine whether and how they take part in methane metabolism in the water columns from the lower Pearl River (freshwater) to the coastal South China Sea (seawater). Quantitative PCR (qPCR) and high-throughput sequencing results showed that the abundance of methanogens decreased with increasing salinity, suggesting that growth of these methanogens in the Pearl River Estuary may be influenced by high salinity. Also, the methane concentration in surface waters was lower than that in near-bottom waters at most sites, suggesting sediment methanogens are a likely source of methane. In the estuarine mixing zone, significantly high methane concentrations existed with the presence of salt-tolerant methanogens (e.g., Methanomicrobiaceae, Methanocella, Methanosaeta and Methanobacterium) and methanotrophs (e.g., Methylocystis and Methylococcaceae), which were found in brackish habitats. Furthermore, a number of methanotrophic OTUs (from pmoA gene sequence data) had specific positive correlations with methanogenic OTUs (from mcrA gene sequence data), and some of these methanogenic OTUs were correlated with concentrations of particulate organic carbon (POC). The results indicate that methanotrophs and methanogens may be intimately linked in methane metabolism attached with particles in estuarine waters.

Genomic adaptation to eutrophication of ammonia-oxidizing archaea in the Pearl River estuary.

Ammonia-oxidizing archaea (AOA) are ubiquitous in natural ecosystems, and they are responsible for a significant fraction of ammonia oxidation globally. Since the first AOA isolate was established a decade ago, molecular surveys of their environmental distribution [based primarily on amplicon sequencing of the amoA, which codes for the alpha subunit of ammonia monooxygenase (AMO)], show that their habitats are believed to range from marine to terrestrial environments. However, the mechanisms of adaptation underpinning to their habitat expansion remain poorly understood. Here, we report that AOA accounts for almost all of the ammonia oxidizers in the shelf water adjacent to the Pearl River estuary (PRE), with the Nitrosopumilus maritimus SCM1-like (SCM1-like) being the main amoA genotype. Using a metagenomic approach, seven high-quality AOA genomes were reconstructed from the PRE. Phylogenetic analysis indicated that four of these genomes with high completeness were closely affiliated with the Nitrosomatrinus catalina strain SPOT01, which was originally isolated off the coast of California. Genomic comparison revealed that the PRE AOA genomes encoded genes functioning in amino acid synthesis, xenobiotic biodegradation metabolism and transportation of inorganic phosphate and heavy metals. This illustrates the different adaptations of AOA in one of the largest estuaries in China, which is strongly influenced by anthropogenic input. Overall, this study provides additional genomic information about estuarine AOA and highlights the importance of their contribution to nitrification in eutrophic coastal environments.

Distribution of organic carbon and lignin in soils in a subtropical small mountainous river basin.

As a unique biomarker of terrigenous organic matter (OM), lignin has provided valuable information for tracing the sources of OM in land to ocean transfer. Oceanian small mountainous rivers (SMRs) are characterized by extremely high erosional rate and quick change in microclimate within watershed, which may potentially affect the distribution of soil OC and lignin concentrations and compositions. Bulk OC% and lignin were determined on surface soils and soil profiles from a Taiwanese SMR (Jhuoshuei River) and nearby region along a large altitudinal gradient (3-3176 m) to investigate the influence of microclimate on soil OC and lignin. Both surface soils OC% and lignin increased in higher altitude, suggesting higher preservation of OM in the cold region. Variations in lignin vegetation indices (S/V and C/V) in surface soils generally reflect the vegetation change in this river basin, and were more affected by precipitation seasonality than mean annual precipitation. Lignin concentration decreased with depth, along with a decrease in S/V and C/V and an increase in degradation indices ((Ad/Al)v and DHBA/V), reflecting a decreased input and/or biodegradation of lignin in subsoils. Our survey on soil lignin in Taiwan SMR provided the basis for utilizing lignin to trace the source of OC in land to ocean transfer as well as paleo-climate and paleo-vegetation reconstruction study in Taiwan SMRs.

Eutrophication-Driven Hypoxia in the East China Sea off the Changjiang Estuary.

Coastal hypoxia is an increasingly recognized environmental issue of global concern to both the scientific community and the general public. We assessed the relative contributions from marine and terrestrially sourced organic matter that were responsible for oxygen consumption in a well-studied seasonal coastal hypoxic zone, the East China Sea off the Changjiang Estuary. Our fieldwork was conducted in August 2011 during reinstatement of a subsurface hypoxia, when we observed a continuous decline of dissolved oxygen along with production of dissolved inorganic carbon resulting from organic carbon remineralization. On the basis of a three end-member mixing model and determinations of the stable isotopic compositions of dissolved inorganic carbon (δ(13)CDIC), the end product of particulate organic carbon (POC) degradation, we quantified the δ(13)C value of the remineralized organic carbon (δ(13)COCx), which was -18.5 ± 1.0‰. This isotopic composition was very similar to the δ(13)C of marine sourced POC produced in situ (-18.5 ± 0.3‰) rather than that of the terrestrially sourced POC (-24.4 ± 0.2‰). We concluded that marine-sourced organic matter, formed by eutrophication-induced marine primary production, was the dominant oxygen consumer in the subsurface hypoxic zone in the East China Sea off the Changjiang Estuary.

Linking secondary structure of individual size distribution with nonlinear size-trophic level relationship in food webs.

Existing individual size distribution (ISD) theories assume that the trophic level (TL) of an organism varies as a linear function of its log-transformed body size. This assumption predicts a power-law distribution of the ISD, i.e., a linear relationship between size and abundance in log space. However, the secondary structure of ISD (nonlinear dome shape structures deviating from a power-law distribution) is often observed. We propose a model that extends the metabolic theory to link the secondary structure of ISD to the nonlinear size-TL relationship. This model is tested with empirical data collected from a subtropical reservoir. The empirical ISD and size-TL relationships were constructed by FlowCAM imaging analysis and stable isotope analyses, respectively. Our results demonstrate that the secondary structure of ISD can be predicted from the nonlinear function of size-TL relationship and vice versa. Moreover, these secondary structures arise due to (1) zooplankton omnivory and (2) the trophic interactions within microbial food webs.

Trophic niche width increases with bill-size variation in a generalist passerine: a test of niche variation hypothesis.

The niche variation hypothesis (NVH) predicts that populations with wider niches are phenotypically more variable than populations with narrower niches, which is frequently used to explain diversifying processes such as ecological release. However, not all empirical evidence supports the NVH. Furthermore, a relationship between population phenotypic variation and niche width can be caused by sexual selection or environmental gradients, which should be carefully considered along with competition in explaining niche variation. In this study, we used eight populations of a generalist passerine species, Paradoxornis webbianus (vinous-throated parrotbill), to test the NVH. We assessed evidence of ecological sexual dimorphism and environmental gradients in bill morphology of P. webbianus. A total of 170 P. webbianus from eight sites ranging 24-2668 m in altitude were included in this study. We used two principal components to quantify bill morphology: one describes bill size and the other describes bill slenderness. We used stable carbon and nitrogen isotope values of bird feathers to quantify trophic positions, and we estimated population trophic niche width using Bayesian standardized ellipse area. Paradoxornis webbianus with larger and more slender bills fed at higher trophic levels and population trophic niche width tended to increase with bill-size variation, supporting the NVH. The males had larger bills and marginally higher nitrogen isotope values than the females, suggesting ecological sexual dimorphism. Despite a positive correlation between bill size and wing length indicating sexual selection for larger male size, only three of the eight populations showed both male-biased bill size and male-biased wing length. Sexual dimorphism explained 13%-64% of bill-size variation across sites, suggesting its role in niche variation could vary greatly among populations. The variation in bill slenderness in P. webbianus increased with elevation. However, neither bill-size variation nor trophic niche width changed with elevation. Therefore, environmental gradients that could be reflected in the elevation are not likely to drive the observed morphological and niche variation. This study provides an empirical case for the NVH and highlights the importance of investigating sexual dimorphism and environmental gradients in studies of niche dynamics.

The external/internal sources and sinks of greenhouse gases (CO2, CH4, N2O) in the Pearl River Estuary and adjacent coastal waters in summer.

Estuary acts as a hotspot of greenhouse gases (GHGs, including CO2, CH4 and N2O) to the atmosphere. However, the GHGs budgets, including input/output fluxes through interfaces and biogeochemical source/sink processes in water columns, of the estuarine systems are still not well constrained due to the lacking of comprehensive observational data. Here, we presented the spatial distributions of GHGs of surface/bottom water and sediment porewater along the Pearl River Estuary (PRE) and adjacent region during summertime. The incorporation of the monitoring for the sediment-water interface (SWI) with these of the water-air interface (WAI) allows us to close the budget revealing additional information of internal consumption/production processes of the three GHGs. The oversaturated CO2 (481-7573 µatm), CH4 (289-16,990 %) and N2O (108-649 %) in surface water suggested PRE is a significant GHGs source to the atmosphere, in which CO2 is the major contributor accounting for 90 % of total global warming potential (GWP), leaving 2.8 % from CH4, and 7.2 % from N2O. Addition to the river input, the SWI releases GHGs to the overlying water with fluxes of 3.5 × 107, 10.8 × 104 and 0.7 × 104 mol d-1 for CO2, CH4 and N2O, respectively. Although all three GHGs exhibited emission to the atmosphere, our mass balance calculation showed that 16.9× 107 mol d-1 of CO2 and 1.0 × 104 mol d-1 of N2O were consumed, respectively, inside the estuary water body, while extra-production (13.8 × 104 mol d-1) of CH4 was demanded in the water body to support its output flux. This is the first experiment quantitatively assessing the importance of internal carbon and nitrogen biogeochemical processes in the PRE. Our finding is of guiding significance to constrain the GHGs budget and draw up realistic pathways for modeling works of GHGs prediction.

Assessment of Secondary Sulfate Aqueous-Phase Formation Pathways in the Tropical Island City of Haikou: A Chemical Kinetic Perspective.

Sulfate (SO42-) is an essential chemical species in atmospheric aerosols and plays an influential role in their physical-chemical characteristics. The mechanisms of secondary SO42- aerosol have been intensively studied in air-polluted cities. However, few studies have focused on cities with good air quality. One-year PM2.5 samples were collected in the tropical island city of Haikou, and water-soluble inorganic ions, as well as water-soluble Fe and Mn, were analyzed. The results showed that non-sea-salt SO42- (nss-SO42-) was the dominant species of water-soluble inorganic ions, accounting for 40-57% of the total water-soluble inorganic ions in PM2.5 in Haikou. The S(IV)+H2O2 pathway was the main formation pathway for secondary SO42- in wintertime in Haikou, contributing to 57% of secondary SO42- formation. By contrast, 54% of secondary SO42- was produced by the S(IV)+Fe×Mn pathway in summer. In spring and autumn, the S(IV)+H2O2, S(IV)+Fe×Mn, and S(IV)+NO2 pathways contributed equally to secondary SO42- formation. The ionic strength was the controlling parameter for the S(IV)+NO2 pathway, while pH was identified as a key factor that mediates the S(IV)+H2O2 and S(IV)+Fe×Mn pathways to produce secondary SO42-. This study contributes to our understanding of secondary SO42- production under low PM2.5 concentrations but high SO42- percentages.

The underestimated role of manganese in modulating the nutrient structure in a eutrophic seasonally-stratified reservoir.

Accumulation and subsequent release of nutrients have great potential to trigger algal blooms in lakes and reservoirs. We conducted high vertical resolution (2 m interval) monitoring at ∼monthly intervals over a year for hydrological parameters, Chl-a, ammonium (NH4+), nitrate (NO3-) and different species of phosphorus (P) and manganese (Mn) in a 40-meter-deep subtropical reservoir (Shanmei Reservoir) in Fujian, southern China. In this seasonally stratified reservoir featured with high nutrient loading, the consistent trend in the ratio of dissolved inorganic nitrogen (DIN) to dissolved inorganic phosphorus (DIP) between the euphotic zone and the hypolimnion, coupled with its mirrored correlation with Chl-a concentration indicates that upward flux from the hypolimnion affects phytoplankton growth in the euphotic zone. The monthly variation of the depth-integrated multiple species of N and P indicates that during the stratification period in the hypoxic hypolimnion, approximately 80% of the DIP is removed, leading to a remarkable decoupling phenomenon between NH4+ and DIP. This process effectively increases the ratio of DIN to DIP in the hypolimnion, thereby significantly reducing the potential of algal blooms caused by the upward flux. A robust positive linear correlation between iron-manganese bound phosphorus (CBD-P) and particulate Mn was observed during stratification period implying that DIP was scavenged by sediment-released Mn throughout the water column. Vertical profiles during stratification showed that upward diffusion of Mn2+ facilitated the formation of Mn oxide zones near the oxycline. The most significant decrease in DIP inventory occurs when Mn oxide zones migrate either upwards from the bottom or downwards from the oxycline, indicating that the migration of Mn oxides on the vertical profile is a key factor in the decoupling of NH4+and DIP. Our findings underscore the importance of Mn cycling as an underappreciated DIP self-immobilization process in the water column of reservoirs characterized by high nutrient loading. Furthermore, we propose that denitrification and Mn cycling establish a consecutive feedback mechanism, preventing excessive nutrient accumulation in low oxygen bottom water. In the context of global changes, we anticipate a heightened prominence of this feedback mechanism.

Seamounts generate efficient active transport loops to nourish the twilight ecosystem.

Seamounts are ecological oases nurturing abundant fisheries resources and epibenthic megafauna in the vast oligotrophic ocean. Despite their significance, the formation mechanisms underlying these seamount ecological oases remain uncertain. To shed light on this phenomenon, this study conducted interdisciplinary in situ observations focusing on a shallow seamount in the oligotrophic ocean. The findings show that the seamount's topography interferes with the oceanic current to generate lee waves, effectively enhancing the nutrient supply to the euphotic layer downstream of the seamount. This continuous supply enhances phytoplankton biomass and subsequently the grazing and diurnal vertical migration of zooplankton, rapidly transporting the augmented phytoplankton biomass to the aphotic layer. Unlike the cyclonic eddies that move in the upper ocean, seamounts stand at fixed locations creating a more efficient and steady active transport loop. This active transport loop connects the euphotic and twilight zones, potentially conveying nourishment to benthic ecosystems to create stereoscopic oases in the oligotrophic ocean.

Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth.

Land-ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.

What controls aerosol δ15N-NO3-? NOx emission sources vs. nitrogen isotope fractionation.

Atmospheric δ15N-NO3- has been used to reveal NOx (NO + NO2) sources as NO3- is the ultimate sink of NOx. However, it remains questionable whether the nitrogen isotope fractionation among NOy (NO, NO2, NO3, N2O5, HNO3 and NO3-) engender the misjudgment of NOx emission sources by affecting δ15N-NOy. To explore this issue, we integrated the dataset of aerosol δ15N-NO3- values and ratios of fNO2 (fNO2 = NO2/(NO2 + NO)), calculated the nitrogen isotope fractionation factors (Δs) among NOy, compared the total energy consumption in Beijing-Tianjin-Hebei region (BTH) from 2013 to 2018. Results showed that, although the total energy consumption structure changed from 2013 to 2018 in BTH, there were fewer interannual variances of aerosol δ15N-NO3- values. Nitrogen isotope fractionation factors between NO and NO2 (Δ0), NO2 and NO3 (Δ2), NO2 and N2O5 (Δ3), NO2 and ClONO2 (Δ4) also displayed less interannual variations from 2013 to 2018 in BTH. But both aerosol δ15N-NO3- and Δs displayed significant seasonal patterns, and there was significant relationship between monthly aerosol δ15N-NO3- and Δs, which suggested that Δs have important influence on shaping aerosol δ15N-NO3- and further discriminating NOx emission sources. This study implies that we should refine the Δs when employing atmospheric δ15N-NO3- to quantify NOx source allocation.

Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary.

In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.

Molecular level characterization of the biolability of rainwater dissolved organic matter.

The atmospheric wet deposition has been recognized as a significant allochthonous source of dissolved organic carbon (DOC) to the ocean. However, few studies have examined the biolability of rainwater dissolved organic matter (DOM) at the molecular level. Rainwater samples were collected and incubated with ambient microbes. DOC, UV-vis spectroscopy, formic acid (FA), acetic acid (AA), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS) were applied. Approximately 50 ± 16 % of rainwater DOC and ~90 % of FA and AA were bioconsumed within 28 days. The contribution of FA and AA to the total BDOC was ~30 %, which was the largest known biolabile fraction in rainwater DOC. In contrast, only approximately 15 % of formulae identified by FT-ICRMS were consumed, which were characterized by higher saturation, higher heteroatom content and lower modified aromaticity. Among the major high molecular weight secondary organic carbon (HWW-SOC)-like compounds, organosulfate contained the largest fraction of consumed formulae, while biogenic volatile organic-derived CHO compounds had the lowest. Our study for the first time provided both quantitative and qualitative understanding of the bioavailability of rainwater DOM, which is essential for understanding their effects on the biogeochemical cycles and the environmental health in the receiving waters.

Nitrogen fixation and diazotroph diversity in groundwater systems.

Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.

Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris.

Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb 3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.