Explaining nitrogen turnover in sediments and water through variations in microbial community composition and potential function.

Anthropogenic activities greatly impact nitrogen (N) biogeochemical cycling in aquatic ecosystems. High N concentrations in coastal aquaculture waters threaten fishery production and aquaculture ecosystems and have become an urgent problem to be solved. Existing microbial flora and metabolic potential significantly regulate N turnover in aquatic ecosystems. To clarify the contribution of microorganisms to N turnover in sediment and water, we investigated three types of aquaculture ecosystems in coastal areas of Guangdong, China. Nitrate nitrogen (NO3--N) was the dominant component of total nitrogen in the sediment (interstitial water, 90.4%) and water (61.6%). This finding indicates that NO3--N (1.67-2.86 mg/L and 2.98-7.89 mg/L in the sediment and water) is a major pollutant in aquaculture ecosystems. In water, the relative abundances of assimilation nitrogen reduction and aerobic denitrifying bacteria, as well as the metabolic potentials of nitrogen fixation and dissimilated nitrogen in fish monoculture, were only 61.0%, 31.5%, 47.5%, and 27.2% of fish and shrimp polyculture, respectively. In addition, fish-shrimp polyculture reduced NO3--N content (2.86 mg/L) compared to fish monoculture (7.89 mg/L), which was consistent with changes in aerobic denitrification and nitrate assimilation, suggesting that polyculture could reduce TN concentrations in water bodies and alleviate nitrogen pollution risks. Further analysis via structural equation modeling (SEM) revealed that functional pathways (36% and 31%) explained TN changes better than microbial groups in sediment and water (13% and 11%), suggesting that microbial functional capabilities explain TN better than microbial community composition and other factors (pH, O2, and aquaculture type). This study enhances our understanding of nitrogen pollution characteristics and microbial community and functional capabilities related to sediment-water nitrogen turnover in three types of aquaculture ecosystems, which can contribute to the preservation of healthy coastal ecosystems.

Cable bacteria accelerate the anaerobic removal of pyrene in black odorous river sediments.

Cable bacteria play an essential role in biogeochemical processes in sediments by long-distance electron transport (LDET). A potential relationship has been found between cable bacteria and organic contaminant removal; however, the mechanisms remain unclear. In this study, the response of cable bacteria to pyrene was investigated in sediments with and without pyrene, and the effect of cable bacteria on pyrene removal was explored by connecting and blocking the paths of cable bacteria to the suboxic zones. The results showed that pyrene significantly influenced the microbial community structure and the composition of cable bacteria. The pyrene removal efficiencies significantly increased with the enrichment of cable bacteria, while sulfur-reducing microorganisms and aromatic compound degraders were also significantly enriched and correlated with cable bacteria abundance. Metagenomic analysis showed that cable bacteria have a potential LDET-bound acetate/formate respiratory pathway to gain energy. The presence of pyrene probably selects and enriches cable bacteria with a high tolerance to organic contaminants and changes the related functional microbial community, leading to the acceleration of pyrene removal. This study provides new insights into the interaction mechanisms between contaminants and cable bacteria, shedding light on the applications of cable bacteria in the bioremediation of contaminants in sediments.

Tabrizicola rongguiensis sp. nov., isolated from the sediment of a river in Ronggui, Foshan city, China.

A novel Gram-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterium, designated J26T, was isolated from the sediment of a river in Ronggui, Foshan city, China. Strain J26T grew optimally at 0 % (w/v) NaCl, pH 6.5-7.5, and 30 °C, and it formed milky white irregular colonies on Reasoner's 2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J26T had the highest similarity to Tabrizicola aquatica RCRI19T (97.1 %) and formed a distinct clade in the genus Tabrizicola. Cellular components of J26T supported this strain as a member of the genus Tabrizicola. The predominant fatty acids were C18 : 1 ω7c, C18 : 1 ω7c-11 methyl and C16 : 0. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphorylethanolamine. Ubiquinone Q-10 was the major respiratory quinone, and the DNA G+C content was 64.2 mol%. However, low 16S rRNA gene sequence similarity and average nucleotide identity (73.56 % for ANIb between strain J26T with RCRI19T) demonstrated that strain J26T should be assigned to a novel species. Moreover, the differences between J26T and RCRI19T in terms of physiological and biochemical properties, such as carbon, nitrogen and sulphur metabolism, further supported that J26T represents a novel species, for which the name Tabrizicola rongguiensis sp. nov. is proposed. The type strain is J26T (=GDMCC 1.2843T=KCTC 92112T).

Water quality drives the distribution of freshwater cable bacteria.

Cable bacteria are a group of recently found filamentous sulfide-oxidizing Desulfobulbaceae that significantly impact biogeochemical cycling. However, the limited understanding of cable bacteria distribution patterns and the driving force hindered our abilities to evaluate and maximize their contribution to environmental health. We evaluated cable bacteria assemblages from ten river sediments in the Pearl River Delta, China. The results revealed a clear biogeographic distribution pattern of cable bacteria, and their communities were deterministically assembled through water quality-driven selection. Cable bacteria are diverse in the river sediments with a few generalists and many specialists, and the water quality IV and V environments are the "hot spot." We then provided evidence on their morphology, function, and genome to demonstrate how water quality might shape the cable bacteria assemblages. Reduced cell width, inhibited function, and water quality-related adaptive genomic traits were detected in sulfide-limited water quality III and contaminant-stressed water quality VI environments. Specifically, those genomic traits were contributed to carbon and sulfur metabolism in the water quality III environment and stress resistance in the water quality VI environment. Overall, these findings provided a helpful baseline in evaluating the contribution of cable bacteria in the freshwater ecosystem and suggested that their high diversity and flexibility in phylogeny, morphology, and genome allowed them to adapt and contribute to various environmental conditions.

Microbial carriers promote and guide pyrene migration in sediments.

Microbial carriers may co-transport polycyclic aromatic hydrocarbons (PAHs), but lack substantial experimental evidence. Cable bacteria use gliding or twitching motility to access sulfide; hence, they could be important microbial carriers in co-transporting PAHs from the sediment-water interface into suboxic zones. In this study, the effect of cable bacteria on pyrene migration was investigated by connecting or blocking the paths of cable bacteria to the suboxic zones. The results showed that downward migration of pyrene in the connecting groups were significantly higher (17.3-49.2%, p < 0.01) than those in the control groups. Meanwhile, significant downward migration of microbial communities in the connecting groups were also observed, including abundant filamentous-motile microorganisms, especially cable bacteria. The adsorption of surrounding particles by cable bacteria were morphologically evidenced. The biomechanical model based on the Peclet number indicated that filamentous-motile microorganisms demonstrated stronger adsorption ability for pyrene than other microorganisms. Supposedly, the downward migration of microbial communities, especially cable bacteria, significantly enhanced pyrene migration, thus influencing the distribution and ecological risk of pyrene in sediments. This study provides new insights into the important roles of motile microorganisms in the migration of PAHs in sediments, shedding lights on guidance for ecological risk assessment of PAHs.

Synergistic interactions of Desulfovibrio and Petrimonas for sulfate-reduction coupling polycyclic aromatic hydrocarbon degradation.

Microbial sulfate-reduction coupling polycyclic aromatic hydrocarbon (PAH) degradation is an important process for the remediation of contaminated sediments. However, little is known about core players and their mechanisms in this process due to the complexity of PAH degradation and the large number of microorganisms involved. Here we analyzed potential core players in a black-odorous sediment using gradient-dilution culturing, isolation and genomic/metagenomic approaches. Along the dilution gradient, microbial PAH degradation and sulfate consumption were not decreased, and even a significant (p = 0.003) increase was observed in the degradation of phenanthrene although the microbial diversity declined. Two species, affiliated with Desulfovibrio and Petrimonas, were commonly present in all of the gradients as keystone taxa and showed as the dominant microorganisms in the single colony (SB8) isolated from the highest dilution culture with 93.49% and 4.73% of the microbial community, respectively. Desulfovibrio sp. SB8 and Petrimonas sp. SB8 could serve together as core players for sulfate-reduction coupling PAH degradation, in which Desulfovibrio sp. SB8 could degrade PAHs to hexahydro-2-naphthoyl through the carboxylation pathway while Petrimonas sp. SB8 might degrade intermediate metabolites of PAHs. This study provides new insights into the microbial sulfate-reduction coupling PAH degradation in black-odorous sediments.

Vertical profiles and distributions of aqueous endocrine-disrupting chemicals in different matrices from the Pearl River Delta and the influence of environmental factors.

The occurrence and distributions of selected endocrine-disrupting chemicals (EDCs), along with related environmental factors, were investigated in two rivers and six reservoirs in the Pearl River Delta. The vertical profiles of aqueous 4-tert-octylphenol (OP), 4-nonylphenol (NP), and estrone (E1) were constant, with little change in concentration between the surface and the river bottom, while higher aqueous concentrations of bisphenol A (BPA) were found in the bottom layers of the rivers. OP and NP in suspended particulate matter (SPM) were transferred from the surface to the bed layer, ultimately accumulating in the sediment. However, the particulate profiles of BPA and E1 both featured increases from the surface to the bottom layers and attenuation in the river bed. Dissolved oxygen (DO), water temperature, and pH were negatively correlated with the EDC concentrations, and negative relationships between DO and distribution coefficient (Kd) values for OP and NP were found as well. This indicated that these environmental parameters were primarily responsible for the EDC vertical distribution and SPM-water partitioning in the rivers. Positive relationships were observed between chlorophyll a and EDCs in the particulate phase, and the algae/water Kd values for EDCs in reservoirs were comparable to the SPM/water and sediment/water Kd values from the rivers. These results suggest that algae played an important role in regulating the distribution of EDCs in surface waters. Moreover, relationships between UV absorbance and EDCs revealed that π-π interactions were among the dissolved organic carbon (DOC)-EDC binding mechanisms and that DOC fractions with higher degrees of aromaticity and humification possessed higher affinities towards EDCs.

Distribution and partitioning of polybrominated diphenyl ethers in sediments from the Pearl River Delta and Guiyu, South China.

Polybrominated diphenyl ethers (PBDEs) were investigated by GC-NCI-MS in sediments collected from the Pearl River Delta (PRD) and Guiyu town, South China. The concentrations of ∑39PBDEs and BDE 209 were in the ranges of 0.31-38.9 ng g-1 and 12.2-488 ng g-1 in the PRD, and 2.57-21,207 ng g-1 and 7.02-66,573 ng g-1 in Guiyu, respectively. The levels of PBDEs in Dongjiang River (DJ), Zhujiang River (ZJ), and Beijiang River (BJ), and Guiyu (GY) followed the order: GY > DJ > ZJ > BJ. The very high PBDE concentration (87,779 ng g-1) was detected at G1 sediment in Guiyu compared with those in sediments from other regions around the world. The PBDE mixtures detected were mainly comprised of penta-, octa-, and deca-BDEs, in which deca-BDE was the dominant constituent. The abundant congeners, excluding BDE-209, were BDE-47, BDE-99, and BDE-183, suggesting the diverse use of commercial products containing these congeners in this region. The concentrations of major congeners were significantly correlated with total organic carbon (TOC) contents (p < .01). A good regression between the logarithmic TOC-normalized BDE average concentrations and their log Kow confirmed that the sorption of PBDEs on sediment organic matter governed their spatial distribution, transport, and fate in the sediments. Furthermore, risk quotients (RQs) derived from concentrations of PBDEs in sediments from our study may pose high ecological risks to exposure of benthic organisms.

Importance of the structure and nanoporosity of organic matter on the desorption kinetics of benzo[a]pyrene in sediments.

The desorption kinetics and mechanism were investigated using a Tenax extraction technique on different sediments spiked with radiocarbon-labeled benzo[a]pyrene (BaP). Five sedimentary fractions were sequentially fractionated, and the only nonhydrolyzable organic carbon fractions (NHC) were characterized using advanced solid-state 13C nuclear magnetic resonance spectroscopy (NMR), improved six end-member model, and a CO2 gas adsorption technique. The sediments contained high percentages of algaenan and/or sporopollenin but low percentages of black carbon and lignin. A first-order, two-compartment kinetics model described the desorption process very well (R2 > 0.990). Although some of the organic carbon fractions were significantly related to the desorption kinetics parameters, the NHC fractions showed the highly significant correlation. Moreover, the nanoporosity or specific surface area (SSA) of the NHC fractions was highly related to their OC contents and aliphatic C (R2 = 0.960, p < 0.01). The multiple regression equations among the desorption kinetics parameters, structural parameters, and nanoporosity were well established (R2=>0.999). Nanoporosity and aromatic C were the dominant contributors. Furthermore, the enhanced percentages of desorbed BaP at elevated temperatures significantly showed a linear regression with the structure and nanoporosity. To our knowledge, the above evidence demonstrates for the first time that the transfer (or diffusion) of BaP in the nanopores of condensed aromatic components is the dominant mechanism of the desorption kinetics of BaP at organic matter particle scale.

Novel Phenanthrene Sorption Mechanism by Two Pollens and Their Fractions.

A pair of pollens (Nelumbo nucifera and Brassica campestris L.) and their fractions were characterized by elemental analysis and advanced solid-state (13)C NMR techniques and used as biosorbents for phenanthrene (Phen). Their constituents were largely aliphatic components (including sporopollenin), carbohydrates, protein, and lignin as estimated by (13)C NMR spectra of the investigated samples and the four listed biochemical classes. The structure of each nonhydrolyzable carbon (NHC) fraction is similar to that of sporopollenin. The sorption capacities are highly negatively related to polar groups largely derived from carbohydrates and protein but highly positively related to alkyl carbon, poly(methylene) carbon, and aromatic carbon largely derived from sporopollenin and lignin. The sorption capacities of the NHC fractions are much higher than previously reported values, suggesting that they are good sorbents for Phen. The Freundlich n values significantly decrease with increasing concentrations of poly(methylene) carbon, alkyl C, aromatic moieties, aliphatic components, and the lignin of the pollen sorbents, suggesting that aliphatic and aromatic structures and constituents jointly contribute to the increasing nonlinearity. To our knowledge, this is the first investigation of the combined roles of alkyl and aromatic moiety domains, composition, and accessibility on the sorption of Phen by pollen samples.

Role of structure, accessibility and microporosity on sorption of phenanthrene and nonylphenol by sediments and their fractions.

To better understand interaction mechanism of sediment organic matter with hydrophobic organic compounds, sorption of phenanthrene (Phen) and nonylphenol (NP) by bulk sediments and their fractions was investigated. Three surface sediments were selectively fractionated into different organic fractions, including the demineralized carbon (DM), lipid free carbon (LF), lipid (LP), and nonhydrolyzable carbon (NHC) fractions. The structure and microporosity of the isolated fractions were characterized by NMR and CO2 adsorption techniques, and used as sorbents for Phen and NP. The calculated micropore volumes (Vo) and specific surface area (SSA) values are positively related to the concentrations of aromatic C and char for the DM, LF and NHC fractions, suggesting that aromatic moieties and char component significantly contribute to the microporosity. The LF fractions exhibit greater sorption affinity than the DM fractions do, indicating that the presence of LP could block the accessibility of sorption sites for Phen and NP. Significant and positive correlations among log K'FOC values for Phen and NP and aromatic carbon and char contents, and Vo and SSA values suggest the aromatic moieties and microporosity dominate their sorption of HOCs by sediment organic matter (SOM). As the NHC fractions have much stronger sorption than other fractions do, they dominate the overall sorption by the bulk samples. This study indicated that the important roles of aromatic moieties, accessibility, and microporosity in the sorption of HOCs by SOM.

Multiphase partitioning and risk assessment of endocrine-disrupting chemicals in the Pearl River, China.

Multiphase partitioning of endocrine-disrupting chemicals (EDCs) in the Pearl River (China) were investigated. The colloidal concentrations for 4-tert-octylphenol, 4-nonylphenol, bisphenol A (BPA), and estrone (E1) were in the ranges of 0.2 ng/L to 0.8 ng/L, 23.2 ng/L to 108 ng/L, 2.3 ng/L to 97.6 ng/L, and not detectable (nd) to 0.32 ng/L, respectively; for truly dissolved concentrations, the ranges were 0.5 ng/L to 5.4 ng/L, 39 ng/L to 319 ng/L, 13.7 ng/L to 91.2 ng/L, and nd to 1.2 ng/L, respectively. Positive correlations of EDCs with colloidal organic carbon (COC) were observed. The in situ COC normalized partitioning coefficients (log KCOC ) for 4-tert-octylphenol (5.35 ± 0.42), 4-nonylphenol (5.69 ± 0.50), and BPA (5.51 ± 0.77) were within the ranges reported by other studies, whereas they were 1 to 2 orders of magnitude higher than their particulate/truly dissolved phase partition coefficients (log KOCint), revealing much strong sorption of EDCs by aquatic colloids. Moreover, colloid-bound percentages of 4-tert-octylphenol, 4-nonylphenol, and BPA ranged, respectively, from 6.9% to 36.4%, from 16.7% to 63.1%, and from 3.6% to 52.4%; their estimated mass fractions were 0.29 ± 0.21, 0.38 ± 0.26, and 0.39 ± 0.33, respectively. Obviously the colloid-bound fractions are significant. Furthermore, a medium risk of estrogenic effects was estimated from the truly dissolved concentrations of EDCs in the Pearl River, which was lower than the estimated high risk according to the conventionally dissolved concentrations. It is suggested that the presence of colloids be incorporated into future water quality prediction and ecological risk assessment. Environ Toxicol Chem 2016;35:2474-2482. © 2016 SETAC.