Deletion of ArmPT, a LamB-like protein, increases cell membrane permeability and antibiotic sensitivity in Vibrio alginolyticus.

Vibrio bacterial species are dominant pathogens in mariculture animals. However, the extensive use of antibiotics and other chemicals has increased drug resistance in Vibrio bacteria. Despite rigorous investigative studies, the mechanism of drug resistance in Vibrio remains a mystery. In this study, we found that a gene encoding LamB-like outer membrane protein, named ArmPT, was upregulated in Va under antibiotic stress by RT-qPCR. We speculated that ArmPT might play a role in Va's drug resistance. Subsequently, using ArmPT gene knockout and gene complementation experiments, we confirmed its role in resistance against a variety of antibiotics, particularly kanamycin (KA). Transcriptomic and proteomic analyses identified 188 and 83 differentially expressed genes in the mutant strain compared with the wild-type (WT) before and after KA stress, respectively. Bioinformatic analysis predicted that ArmPT might control cell membrane permeability by changing cadaverine biosynthesis, thereby influencing the cell entry of antibiotics in Va. The higher levels of intracellular reactive oxygen species and the infused content of KA showed that antibiotics are more likely to enter the Va mutant strain. These results uncover the drug resistance mechanism of Va that can also exist in other similar pathogenic bacteria.

Novosphingobium mangrovi sp. nov., isolated from mangrove sediment.

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated as HK4-1T, was isolated from mangrove sediments in Hong Kong, PR China. Based on 16S rRNA gene sequence data, strain HK4-1T was found to belong to the genus Novosphingobium, family Erythrobacteraceae, and showed high similarity to Novosphingobium chloroacetimidivorans BUT-14T (96.88 %) and Novosphingobium indicum H25T (96.88 %). The G+C content of the whole genome of strain HK4-1T was 64.05 mol%. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and two unknown lipids. The predominant respiratory quinone was Q-10. Based on genomic, phylogenetic, phenotypic, physiological and chemotaxonomic data, strain HK4-1T should be classified as representing a novel species of the genus Novosphingobium, for which the name Novosphingobium mangrovi sp. nov. is proposed. The type strain of Novosphingobium mangrovi sp. nov. is HK4-1T (=MCCC 1K08252T=JCM 35764T).

Ecological distribution and function of comammox Nitrospira in the environment.

Complete ammonia oxidizers (Comammox) are of great significance for studying nitrification and expanding the understanding of the nitrogen cycle. Moreover, Comammox bacteria are also crucial in natural and engineered environments due to their role in wastewater treatment and maintaining the flux of greenhouse gases to the atmosphere. However, only few studies are there regarding the Comammox bacteria and their role in ammonia and nitrite oxidation in the environment. This review mainly focuses on summarizing the genomes of Nitrospira in the NCBI database. Ecological distribution of Nitrospira was also reviewed and the influence of environmental parameters on genus Nitrospira in different environments has been summarized. Furthermore, the role of Nitrospira in carbon cycle, nitrogen cycle, and sulfur cycle were discussed, especially the comammox Nitrospira. In addition, the overviews of current research and development regarding comammox Nitrospira, were summarized along with the scope of future research. KEY POINTS: • Most of Comammox Nitrospira are widely distributed in both aquatic and terrestrial ecosystems, but it has been studied less frequently in the extreme environments. • Comammox Nitrospira can be involved in different nitrogen transformation process, but rarely involved in nitrogen fixation. • The stable isotope and transcriptome techniques are important methods to study the metabolic function of comammox Nitrospira.

Cytochrome P450 for environmental remediation: catalytic mechanism, engineering strategies and future prospects.

Environmental pollution is a global concern. Various organic compounds are released into the environment through wastewater, waste gas, and waste residue, ultimately accumulating in the environment and the food chain. This poses a significant threat to both human health and ecology. Currently, a growing body of research has demonstrated that microorganisms employ their Cytochrome P450 (CYP450) system for biodegradation, offering a crucial approach for eliminating these pollutants in environmental remediation. CYP450, a ubiquitous catalyst in nature, includes a vast array of family members distributed widely across various organisms, including bacteria, fungi, and mammals. These enzymes participate in the metabolism of diverse organic compounds. Furthermore, the rapid advancements in enzyme and protein engineering have led to increased utilization of engineered CYP450s in environmental remediation, enhancing their efficiency in pollutant removal. This article presents an overview of the current understanding of various members of the CYP450 superfamily involved in transforming organic pollutants and the engineering of biodegrading CYP450s. Additionally, it explores the catalytic mechanisms, current practical applications of CYP450-based systems, their potential applications, and the prospects in bioremediation.

Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments.

Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO2-, and NO3-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO2-, and NO3- are important shapers of nitrifier communities in mangroves.

Transformation of HBCDs by Rhodococcus sp. stu-38.

1,2,5,6,9,10-Hexabromocyclododecanes (HBCDs) are brominated flame retardants causing serious environmental pollution. HBCDs in the environment could be transformed to various products. Identification of transformation products has been performed using various mass-spectrometric techniques. However, bacterial transformation of HBCDs yielding low-level products was not well studied. In this paper, a Rhodococcus strain stu-38 which could stereoselectively transform HBCDs in mineral salt medium, seawater, and growth medium was isolated. Seven potential biotransformation products of HBCDs were identified by using GC-MS. These products, including brominated alkenes, dibromocyclododecadiene and bromocyclododecatriene; brominated alkenols, bromocyclododecadienol and bromocyclododecatrienol; fully debrominated compounds, cyclododecadiendiol, 1,2-epoxy-5,9-cyclododecadiene, and cyclododecadienol, were presented in rather low level which could lead to false negative results. The low-level transformation products should not be ignored because their toxicity was less assessment. This research highlighted identification of the low-level transformation products to reveal the complicated stereoselective biotransformation of HBCDs.

Oxidization of benzo[a]pyrene by CYP102 in a novel PAHs-degrader Pontibacillus sp. HN14 with potential application in high salinity environment.

Benzo [a]pyrene (BaP) is a type of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) with potent carcinogenicity; however, there are limited studies on its degradation mechanism. Here, a strain of Pontibacillus sp. HN14 with BaP degradation ability was isolated from mangrove sediments in Dongzhai Port, Hainan Province. Our study showed that biodegradation efficiencies reached 42.15% after Pontibacillus sp. HN14 was cultured with 20 mg L-1 BaP as the sole carbon source for 25 days and still had degradability of BaP at a 25% high salinity level. Moreover, 9,10-dihydrobenzo [a]pyrene-7(8H)-one, an intermediate metabolite, was detected during BaP degradation in the HN14 strain. Genome analysis identified a gene encoding the CYP102(HN14) enzyme. The results showed that the E. coli strain with CYP102(HN14) overexpression could transfer BaP to 9,10-dihydrobenzo [a]pyrene-7(8H)-one with a conversion rate of 43.5%, indicating that CYP102(HN14) played an essential role in BaP degradation in Pontibacillus sp. HN14. Thus, our results provide a novel BaP biodegradation molecule, which could be used in BaP bioremediation in high salinity conditions. This study is the first to show that CYP102(HN14) had the BaP oxidization ability in bacteria. CYP102(HN14) could be essential in removing PAHs in saline-alkali soil and other high salt environments through enzyme immobilization.

Biotransformation strategies for steroid estrogen and androgen pollution.

The common steroid hormones are estrone (E1), 17ß-estradiol (E2), estriol (E3), 17α-ethinylestradiol (EE2), and testosterone (T). These steroids are reported to contaminate the environment through wastewater treatment plants. Steroid estrogens are widespread in the aquatic environment and therefore pose a potential risk, as exposure to these compounds has adverse impacts on vertebrates. Excessive exposure to steroid estrogens causes endocrine disruption in aquatic vertebrates, which affects the normal sexual life of these animals. Steroid pollutants also cause several health problems in humans and other animals. Microbial degradation is an efficient method for removing hormone pollutants from the environment by remediation. Over the last two decades, microbial metabolism of steroids has gained considerable attention due to its higher efficiency to reduce pollutants from the environment. The present review is focused on the major causes of steroid pollution, concentrations of these pollutants in surface water, groundwater, drinking water, and wastewater, their effect on humans and aquatic animals, as well as recent efforts by various research groups that seek better ways to degrade steroids by aerobic and anaerobic microbial systems. Detailed overview of aerobic and anaerobic microbial biotransformation of steroid estrogens and testosterone present in the environment along with the active enzyme systems involved in these biotransformation reactions is described in the review article, which helps readers to understand the biotransformation mechanism of steroids in depth. Other measures such as co-metabolic degradation, consortia degradation, algal, and fungal steroid biotransformation are also discussed in detail.

NarL, a Novel Repressor for CYP108j1 Expression during PAHs Degradation in Rhodococcus sp. P14.

Rhodococcus sp. P14 was isolated from crude-oil-contaminated sediments, and a wide range of polycyclic aromatic hydrocarbons (PAHs) could be used as the sole source of carbon and energy. A key CYP450 gene, designated as cyp108j1 and involved in the degradation of PAHs, was identified and was able to hydroxylate various PAHs. However, the regulatory mechanism of the expression of cyp108j1 remains unknown. In this study, we found that the expression of cyp108j1 is negatively regulated by a LuxR (helix-turn-helix transcription factors in acyl-homoserine lactones-mediated quorum sensing) family regulator, NarL (nitrate-dependent two-component regulatory factor), which is located upstream of cyp108j1. Further analysis revealed that NarL can directly bind to the promoter region of cyp108j1. Mutational experiments demonstrated that the binding site between NarL and the cyp108j1 promoter was the palindromic sequence GAAAGTTG-CAACTTTC. Together, the finding reveal that NarL is a novel repressor for the expression of cyp108j1 during PAHs degradation.

Isolation and characterization of a marine testosterone-degrading bacterium: Vibrio sp. N3.

Steroids, including testosterone, estrone, 17ß-estradiol, estriol and 17ß-ethinyl estradiol, are harmful not only to the population dynamics of aquatic life forms but also to public health. In this study, a marine testosterone-degrading bacterium (strain N3) was isolated from Nanao Island in the South China Sea. In addition, the strain could also use 17ß-estradiol (E2), 17ß-ethinyl estradiol (EE2), estriol (E3) or cholesterol as a sole carbon source. According to the 16S rRNA gene sequence analysis, strain N3 was identified as Vibrio sp. Further characterization showed that the strain is aerobic, gram-negative, and mobile and exhibits resistance to ampicillin, carbenicillin, penicillin and spectinomycin. For enhancing its capacity of testosterone degradation, the Plackett-Burman factorial design and the central composite design were used to optimize the culture condition. Under optimal conditions, 92% of testosterone was degraded by Vibrio sp. N3 in 48h.

Anaerobic biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a facultative anaerobe Pseudomonas sp. JP1.

Polycyclic aromatic hydrocarbons (PAHs) are harmful persistent organic pollutants, while the high-molecular-weight (HMW) PAHs are even more detrimental to the environment and human health. However, microbial anaerobic degradation of HMW PAHs has rarely been reported. One facultative anaerobe Pseudomonas sp. JP1 was isolated from Shantou Bay, Shantou, China, which could degrade a variety of HMW PAHs. After 40 days cultivation with strain JP1, anaerobic biodegradation rate of benzo[a]pyrene (BaP), fluoranthene, and phenanthrene was 30, 47, and 5 %, respectively. Consumption of nitrate as the electron acceptor was confirmed by N-(1-naphthyl) ethylenediamine spectrophotometry. Supplementation of sodium sulfite, maltose, or glycine, and in a salinity of 0-20 ‰ significantly stimulated anaerobic degradation of BaP. Lastly, the anaerobic degradation metabolites of BaP by strain JP1 were investigated using GC/MS, and the degradation pathway was proposed. This study is helpful for further studies on the mechanism of anaerobic biodegradation of PAHs.

The unique biodegradation pathway of benzo[a]pyrene in moderately halophilic Pontibacillus chungwhensis HN14.

Benzo[a]pyrene (BaP), as the typical representative of polycyclic aromatic hydrocarbons (PAHs), is a serious hazard to human health and natural environments. Though the study of microbial degradation of PAHs has persisted for decades, the degradation pathway of BaP is still unclear. Previously, Pontibacillus chungwhensis HN14 was isolated from high salinity environment exhibiting a high BaP degradation ability. Here, based on the intermediates identified, BaP was found to be transformed to 4,5-epoxide-BaP, BaP-trans-4,5-dihydrodiol, 1,2-dihydroxy-phenanthrene, 2-carboxy-1-naphthol, and 4,5-dimethoxybenzo[a]pyrene by the strain HN14. Furthermore, functional genes involved in degradation of BaP were identified using genome and transcriptome data. Heterogeneous co-expression of monooxygenase CYP102(HN14) and epoxide hydrolase EH(HN14) suggested that CYP102(HN14) could transform BaP to 4,5-epoxide-BaP, which was further transformed to BaP-trans-4,5-dihydrodiol by EH(HN14). Moreover, gene cyp102(HN14) knockout was performed using CRISPR/Cas9 gene-editing system which confirmed that CYP102(HN14) play a key role in the initial conversion of BaP. Finally, a novel BaP degradation pathway was constructed in bacteria, which showed BaP could be converted into chrysene, phenanthrene, naphthalene pathways for the first time. These findings enhanced our understanding of microbial degradation process for BaP and suggested the potential of using P. chungwhensis HN14 for bioremediation in PAH-contaminated environments.

Novel insights into aerobic 17ß-estradiol degradation by enriched microbial communities from mangrove sediments.

Various persistent organic pollutants (POPs) including estrogens are often enriched in mangrove regions. This research investigated the estrogens pollution levels in six mangroves located in the Southern China. The estrogen levels were found to be in the range of 5.3-24.9 ng/g dry weight, suggesting that these mangroves had been seriously contaminated. The bacterial communities under estrogen stress were further enriched by supplementing 17ß-estradiol (E2) as the sole carbon source. The enriched bacterial communities showed an excellent E2 degradation capacity > 95 %. These communities were able to transform E2 into estrone (E1), 4-hydroxy-estrone, and keto-estrone, etc. 16 S rDNA sequencing and metagenomics analysis revealed that bacterial taxa Oleiagrimonas, Pseudomonas, Terrimonas, and Nitratireductor etc. were the main contributors to estrogen degradation. Moreover, the genes involved in E2 degradation were enriched in the microbial communities, including the genes encoding 17ß-hydroxysteroid dehydrogenase, estrone 4-hydroxylase, etc. Finally, the analyses of functional genes and binning genomes demonstrated that E2 was degraded by bacterial communities via dehydrogenation into E1 by 17ß-hydroxysteroid dehydrogenase. E1 was then catabolically converted to 3aα-H-4α(3'-propanoate)- 7aß-methylhexahydro-1,5-indanedione via 4,5-seco pathway. Alternatively, E1 could also be hydroxylated to keto-estrone, followed by B-ring cleavage. This study provides novel insights into the biodegradation of E2 by the bacterial communities in estrogen-contaminated mangroves.

Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China.

Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.

Biotransformation of HBCDs by the microbial communities enriched from mangrove sediments.

1,2,5,6,9,10-Hexabromocyclododecanes (HBCDs) are a sort of persistent organic pollutants (POPs). This research investigated 12 microbial communities enriched from sediments of four mangroves in China to transform HBCDs. Six microbial communities gained high transformation rates (27.5-97.7%) after 12 generations of serial transfer. Bacteria were the main contributors to transform HBCDs rather than fungi. Analyses on the bacterial compositions and binning genomes showed that Alcanivorax (55.246-84.942%) harboring haloalkane dehalogenase genes dadAH and dadBH dominated the microbial communities with high transformation rates. Moreover, expressions of dadAH and dadBH in the microbial communities and Alcanivorax isolate could be induced by HBCDs. Further, it was found that purified proteins DadAH and DadBH showed high conversion rates on HBCDs in 36 h (91.9 ± 7.4 and 101.0 ± 1.8%, respectively). The engineered Escherichia coli BL21 strains harbored two genes could convert 5.7 ± 0.4 and 35.1 ± 0.1% HBCDs, respectively, lower than their cell-free crude extracts (61.2 ± 5.2 and 56.5 ± 8.7%, respectively). The diastereoisomer-specific transforming trend by both microbial communities and enzymes were γ- > α- > ß-HBCD, differed from α- > ß- > Î³-HBCD by the Alcanivorax isolate. The identified transformation products indicated that HBCDs were dehalogenated via HBr elimination (dehydrobromination), hydrolytic and reductive debromination pathways in the enriched cultures. Two enzymes converted HBCDs via hydrolytic debromination. The present research provided theoretical bases for the biotransformation of HBCDs by microbial community and the bioremediation of HBCDs contamination in the environment.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms.

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Draft genome sequence of Rhodococcus sp. strain P14, a biodegrader of high-molecular-weight polycyclic aromatic hydrocarbons.

The genus Rhodococcus is known for its ability to degrade various xenobiotic compounds. Rhodococcus sp. strain P14 isolated from crude oil-contaminated sediments can degrade mineral oil and polycyclic aromatic hydrocarbons (PAHs). The draft genome sequence of Rhodococcus sp. P14 was obtained using Solexa technology, which provided an invaluable genetic background for further investigation of the ability of P14 to degrade xenobiotic compounds.

Identification of an important function of CYP123: Role in the monooxygenase activity in a novel estradiol degradation pathway in bacteria.

Nowadays, 17ß-estradiol (E2) biodegradation pathway has still not been identified in bacteria. To bridge this gap, we have described a novel E2 degradation pathway in Rhodococcus sp. P14 in this study, which showed that estradiol could be first transferred to estrone (E1) and thereby further converted into 16-hydroxyestrone, and then transformed into opened estrogen D ring. In order to identify the genes, which may be responsible for the pathway, transcriptome analysis was performed during E2 degradation in strain P14. The results showed that the expression of a short-chain dehydrogenase (SDR) gene and a CYP123 gene in the same gene cluster could be induced significantly by E2. Based on gene analysis, this gene cluster was found to play an important role in transforming E2 to 16-hydroxyestrone. The function of CYP123 was unknown before this study, and was found to harbor the activity of 16-estrone hydratase. Moreover, the global response to E2 in strain P14 was also analyzed by transcriptome analysis. It was observed that various genes involved in the metabolism processes, like the TCA cycle, lipid and amino acid metabolism, as well as glycolysis showed a significant increase in mRNA levels in response to strain P14 that can use E2 as the single carbon source. Overall, this study provides us an in depth understanding of the E2 degradation mechanisms in bacteria and also sheds light about the ability of strain P14 to effectively use E2 as the major carbon source for promoting its growth.

Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0.

Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; -0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves. IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms.

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.