Culturable populations of Acinetobacter can promptly respond to contamination by alkanes in mangrove sediments

Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts

Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.

A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains

Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.

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.

Woodchips bioretention column for stormwater treatment: Nitrogen removal performance, carbon source and microbial community analysis

This study chose Oak woodchips and gravel as media filter to enhance the denitrification in the bioretention system (saturated zone 7.7 L) treating synthetic stormwater runoff. It revealed that the denitrification process mainly occurred during the drying phase and enlarging volume of saturated zones to retain more stormwater during storm event was the direct method to promote nitrogen removal of the bioretention system. Nevertheless, it was noted that the nitrogen and dissolved organic carbon would be released into the effluent during the wetting period. The denitrification rate with different nitrate nitrogen (NO₃-N) concentrations did not show the obvious change with zero order kinetics constant of 2.91 mg/L∙d on average. Furthermore, it confirmed that woodchips were degraded and converted to volatile fatty acids (VFAs), especially acetic acid as carbon source, further utilized by the denitrifying bacteria, such as Dechloromonas, Acidoborax, Pseudomonas, Denitratisoma and Acinetobacter. In addition, genera of Lachnospiraceae and Lactobacillus, which had the ability to degrade the macromolecular organic components into low molecular VFAs, were observed in the woodchips bioretention system.

DNA-SIP identification of phenanthrene-degrading bacteria undergoing bioaugmentation and natural attenuation in petroleum-contaminated soil

DNA-stable isotope probing (SIP) with ¹³C labeled phenanthrene (PHE) as substrate was used to identify specific bacterial degraders during natural attenuation (NA) and bioaugmentation (BA) in petroleum contaminated soil. BA, with the addition of a bacterial suspension mixture named GZ, played a significant role in PHE degradation with a higher PHE removal rate (∼90%) than that of NA (∼80%) during the first 3 days, and remarkably altered microbial communities. Of the five strains introduced in BA, only two genera, particularly, Ochrobactrum, Rhodococcus were extensively responsible for PHE-degradation. Six (Bacillus sp., Acinetobacter sp., Xanthomonas sp., Conexibacter sp., Acinetobacter sp. and Staphylococcus sp.) and seven (Ochrobactrum sp., Rhodococcus sp., Alkanindiges sp., Williamsia sp., Sphingobium sp., Gillisia sp. and Massilia sp.) bacteria responsible for PHE degradation were identified in NA and BA treatments, respectively. This study reports for the first time the association of Xanthomonas sp., Williamsia sp., and Gillisia sp. to PHE degradation.

The Study of Hydrogeochemical Environments and Microbial Communities along a Groundwater Salinity Gradient in the Pearl River Delta, China

The salinization of groundwater is an issue in coastal areas because it causes the deterioration of freshwater resources, significantly impacting human livelihoods and ecosystems. This study integrated isotopic geochemical measurements with high-throughput sequencing of 16S rRNA gene amplicons to evaluate the source of groundwater salinity and the influence of hydrogeochemical variations on microbial communities under different salinity gradients in the Pearl River Delta of China. Results showed that the groundwater salinity in this area varied from fresh water in the inland area to brackish water, and then to saline water close to the southeast shoreline. The major ions (Na+, K+, Ca2+, Mg2+, Cl−, NO3−, SO42−, and HCO3−) and isotope analyses (2H, 3H, 18O, and 14C) indicated that the groundwater in the confined aquifer was recharged by local precipitation and seawater. A further 14C analysis showed that the salinity of the groundwater was likely attributed to the Holocene transgression. Analysis of the microbial community showed that γ-proteobacteria were frequently observed in all the groundwater samples, while the other main microbial community at class level varied greatly, from β-proteobacteria in the freshwater wells to ε-proteobacteria in the brackish wells and to Bacilli in the saline wells. Exiguobacterium and Acinetobacter were dominant in saline water and the brackish water sample of Q144, while Sulfuricurvum dominated in the brackish water sample of Q143. Aeromonas, no rank Gallionellaceae, no rank Methylophilaceae, Acidovorax, and Comamonas unevenly thrived in the freshwater samples collected from different locations. Therefore, the distribution of microbial communities reflected the salinity and hydrogeochemical characteristics of a groundwater aquifer, and can be regarded as a potential environmental indicator in the groundwater.

Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis

Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg^-1 sediment day^-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.

Petroleum contamination and bioaugmentation in bacterial rhizosphere communities from Avicennia schaueriana

Anthropogenic activity, such as accidental oil spills, are typical sources of urban mangrove pollution that may affect mangrove bacterial communities as well as their mobile genetic elements. To evaluate remediation strategies, we followed over the time the effects of a petroleum hydrocarbon degrading consortium inoculated on mangrove tree Avicennia schaueriana against artificial petroleum contamination in a phytoremediation greenhouse experiment. Interestingly, despite plant protection due to the inoculation, denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene fragments amplified from the total community DNA indicated that the different treatments did not significantly affect the bacterial community composition. However, while the bacterial community was rather stable, pronounced shifts were observed in the abundance of bacteria carrying plasmids. A PCR-Southern blot hybridization analysis indicated an increase in the abundance of IncP-9 catabolic plasmids. Denaturing gradient gel electrophoresis of naphthalene dioxygenase (ndo) genes amplified from cDNA (RNA) indicated the dominance of a specific ndo gene in the inoculated petroleum amendment treatment. The petroleum hydrocarbon degrading consortium characterization indicated the prevalence of bacteria assigned to Pseudomonas spp., Comamonas spp. and Ochrobactrum spp. IncP-9 plasmids were detected for the first time in Comamonas sp. and Ochrobactrum spp., which is a novelty of this study.

Enhanced degradation of phenolic compounds in coal gasification wastewater by a novel integration of micro-electrolysis with biological reactor (MEBR) under the micro-oxygen condition

The aim of this work was to study an integration of micro-electrolysis with biological reactor (MEBR) for strengthening removal of phenolic compounds in coal gasification wastewater (CGW). The results indicated MEBR achieved high efficiencies in removal of COD and phenolic compounds as well as improvement of biodegradability of CGW under the micro-oxygen condition. The integrated MEBR process was more favorable to improvement of the structural stability of activated sludge and biodiversity of specific functional microbial communities. Especially, Shewanella and Pseudomonas were enriched to accelerate the extracellular electron transfer, finally facilitating the degradation of phenolic compounds. Moreover, MEBR process effectively relieved passivation of Fe-C filler surface and prolonged lifespan of Fe-C filler. Accordingly, the synergetic effect between iron-carbon micro-electrolysis (ICME) and biological action played a significant role in performance of the integrated process. Therefore, the integrated MEBR was a promising practical process for enhancing CGW treatment.

Denitrification behavior and microbial community spatial distribution inside woodchip-based solid-phase denitrification (W-SPD) bioreactor for nitrate-contaminated water treatment

The NO₃^- removal pathway and microorganisms change along with the height of an up-flow W-SPD bioreactor was investigated in this study. Modeling and microbial community analysis were used to analyze the denitrification behavior in W-SPD bioreactor. The results showed that NO₃^- removal rate matched for zero-order (R² > 0.97) and first-order (R² > 0.94) combination Michaelis-Menten kinetics, whereas microbial reaction rate suited for modified logistic model (R² > 0.99). The excellent denitrification performance (92.5%-96.4%) and microorganisms' quantity occurred in the middle of W-SPD bioreactor. Moreover, high-throughput sequencing analysis revealed that dominant denitrifiers, carbonaceous compound degrading bacteria and fermentative bacteria co-existed in W-SPD system, which was vital for efficiently sustainable NO₃^- removal. Hence, aerobic degradation, heterotrophic denitrification and dissimilatory nitrate reduction to ammonium (DNRA) occurred successively along the water direction in the bioreactor, offering reasonable references for W-SPD bioreactor study and application.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Draft Genome Sequence of Acinetobacter calcoaceticus Strain GK1, a Hydrocarbon-Degrading Plant Growth-Promoting Rhizospheric Bacterium

The 3.94-Mb draft genome of Acinetobacter calcoaceticus GK1, a hydrocarbonoclastic plant growth-promoting Gram-negative rhizospheric bacterium, is presented here. Isolated at the Ford Motor Company site in Genk, Belgium, from poplar trees planted on a diesel-contaminated plume, GK1 is useful for enhancing hydrocarbon phytoremediation.

Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives

Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.

Laboratory Maintenance of Acinetobacter baumannii

Acinetobacter baumannii has recently drawn great interest in the microbiology research community due to the increase in clinical antibiotic resistance of this organism, and persistence of this bacterial species in the hospital environment. This unit outlines protocols for the growth and maintenance of A. baumannii in the laboratory.