Degradation of pyrene by Xanthobacteraceae bacterium strain S3 isolated from the rhizosphere sediment of Vallisneria natans: active conditions, metabolite identification, and proposed pathways.

Polycyclic aromatic hydrocarbons (PAHs) were typical environmental contaminants that accumulated continuously in sediment. Microbial degradation is the main way of PAH degradation in the natural environment. Therefore, expanding the available pool of microbial resources and investigating the molecular degrading mechanisms of PAHs are critical to the efficient control of PAH-polluted sites. Here, a strain (identified as Xanthobacteraceae bacterium) with the ability to degrade pyrene was screened from the rhizosphere sediment of Vallisneria natans. Response surface analysis showed that the strain could degrade pyrene at pH 5-7, NaCl addition 0-1.5%, and temperature 25-40 °C, and the maximum pyrene degradation (~ 95.4%) was obtained under the optimum conditions (pH 7.0, temperature 28.5 °C, and NaCl-free addition) after 72 h. Also, it was observed that the effect of temperature on the degradation ratio was the most significant. Furthermore, eighteen metabolites were identified by mass spectrometry, among which (2Z)-2-hydroxy-3-(4-oxo-4H-phenalen-3-yl) prop-2-enoic acid, 7-(carboxymethyl)-8-formyl-1-naphthyl acetic acid, phthalic acid, naphthalene-1,2-diol, and phenol were the main metabolites. And the degradation pathway of pyrene was proposed, suggesting that pyrene undergoes initial ortho-cleavage under the catalysis of metapyrocatechase to form (2Z)-2-hydroxy-3-(4-oxo-4H-phenalen-3-yl) prop-2-enoic acid. Subsequently, this intermediate was progressively oxidized and degraded to phthalic acid or phenol, which could enter the tricarboxylic acid cycle. Furthermore, the pyrene biodegradation by the strain followed the first-order kinetic model and the degradation rate changed from fast to slow, with the rate remaining mostly slow in the later stages. The slow biodegradation rate was probably caused by a significant amount of phenol accumulation in the initial stage of degradation, which resulted in a decrease in bacterial activity or death.

Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone.

Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase (nod) gene from Methylomirabilota has been reported in the anoxic core of ODZs. Here, we show that the most abundantly transcribed nod genes in the Eastern Tropical North Pacific ODZ belong to a new order (UBA11136) of Alphaproteobacteria, rather than Methylomirabilota as previously assumed. Gammaproteobacteria and Planctomycetia also transcribe nod, but at lower relative abundance than UBA11136 in the upper ODZ. The nod-transcribing Alphaproteobacteria likely use formaldehyde and formate as a source of electrons for aerobic respiration, with additional electrons possibly from sulfide oxidation. They also transcribe multiheme cytochrome (here named ptd) genes for a putative porin-cytochrome protein complex of unknown function, potentially involved in extracellular electron transfer. Molecular oxygen for aerobic respiration may originate from nitric oxide dismutation via cryptic oxygen cycling. Our results implicate Alphaproteobacteria order UBA11136 as a significant player in marine nitrogen loss and highlight their potential in one-carbon, nitrogen, and sulfur metabolism in ODZs.IMPORTANCEIn marine oxygen-deficient zones (ODZs), microbes transform bioavailable nitrogen to gaseous nitrogen, with nitric oxide as a key intermediate. The Eastern Tropical North Pacific contains the world's largest ODZ, but the identity of the microbes transforming nitric oxide remains unknown. Here, we show that highly transcribed nitric oxide dismutase (nod) genes belong to Alphaproteobacteria of the novel order UBA11136, which lacks cultivated isolates. These Alphaproteobacteria show evidence for aerobic respiration, using oxygen potentially sourced from nitric oxide dismutase, and possess a novel porin-cytochrome protein complex with unknown function. Gammaproteobacteria and Planctomycetia transcribe nod at lower levels. Our results pinpoint the microbes mediating a key step in marine nitrogen loss and reveal an unexpected predicted metabolism for marine Alphaproteobacteria.

Factors influencing cadmium accumulation in plants after inoculation with rhizobacteria: A meta-analysis.

Rhizobacteria have the potential to enhance phytoremediation by generating substances that stimulate plant development and influence the effectiveness of cadmium (Cd) remediation by adjusting Cd availability via metal solubilization. Furthermore, rhizobacterial inoculation affects plants' metal tolerance and uptake by controlling the expression of several metal transporters, channels, and metal chelator genes. A meta-analysis was conducted to quantitatively assess the effects of rhizobacteria on Cd accumulation in plants using 207 individual observations from 47 articles. This meta-analysis showed an average Cd concentration increase of 8.09 % in plant cells under rhizobacteria treatment. The effects of different plant-microbial interactions on the bioaccumulation of Cd in plants varied. Selecting the proper rhizobacteria-plant association is essential to affect Cd buildup in plant roots and shoots. A more extended planting period (>30 days) and a suitable soil pH (<6, 7-8) would aid in the phytoextraction of Cd from the soil. This study comprehensively and quantitatively investigated the effects of plants, rhizobacteria, soil pH, planting period, experimental sites, and plant organs on plant Cd accumulation. According to the analysis of explanatory factors, plant species, planting period, soil pH, and rhizobacteria species have a more decisive influence on Cd accumulation than other factors. The results provide information for future research on the successful remediation of soils contaminated with Cd. More investigations are required to elucidate the intricate interactions between plant roots and microorganisms.

Pseudomonas fluorescens and L-tryptophan application triggered the phytoremediation potential of sunflower (Heliantus annuus L.) in lead-contaminated soil.

Lead, a toxic heavy metal present in soil, hampers biological activities and affects the metabolism of plants, animals, and human beings. Its higher concentration may disturb the various physio-chemical processes, which result in stunted and poor plant growth. An interactive approach of plant growth promoting rhizobacteria (PGPR) and L-tryptophan can be used to mitigate the lethal effects of lead. A pot experiment was conducted, and two weeks before sowing, the level of lead (300 mg kg-1) was maintained by spiking the PbCl2 salt. Pseudomonas fluorescens and L-tryptophan were applied individually as well as in combination to segregate the effect of both in contaminated soil under a completely Randomized Design (CRD). Statistical analysis revealed that plant growth was significantly reduced up to 22% due to lead contamination. However, the interactive approach of PGPR and L-tryptophan significantly improved the plant growth, physiology, and yield with relative productive index (RPI) under a lead-stressed environment. Moreover, integrated use of PGPR and L-tryptophan demonstrated a considerable increase (22%) in lead removal efficiency (LRE) by improving bioconcentration factor (BCF) and translocation factor (TF) for shoot without increasing the lead concentration in achenes. The reduced lead concentration in achene was due to its immobilization in shoot and root by negatively charged particles and improved the lead sequestration in vegetative parts which abridged the translocation of lead into achenes.

Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica.

Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h-1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.

Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments.

Saltmarshes are highly productive environments, exhibiting high abundances of organosulfur compounds. Dimethylsulfoniopropionate (DMSP) is produced in large quantities by algae, plants, and bacteria and is a potential precursor for dimethylsulfoxide (DMSO) and dimethylsulfide (DMS). DMSO serves as electron acceptor for anaerobic respiration leading to DMS formation, which is either emitted or can be degraded by methylotrophic prokaryotes. Major products of these reactions are trace gases with positive (CO2, CH4) or negative (DMS) radiative forcing with contrasting effects on the global climate. Here, we investigated organic sulfur cycling in saltmarsh sediments and followed DMSO reduction in anoxic batch experiments. Compared to previous measurements from marine waters, DMSO concentrations in the saltmarsh sediments were up to ~300 fold higher. In batch experiments, DMSO was reduced to DMS and subsequently consumed with concomitant CH4 production. Changes in prokaryotic communities and DMSO reductase gene counts indicated a dominance of organisms containing the Dms-type DMSO reductases (e.g., Desulfobulbales, Enterobacterales). In contrast, when sulfate reduction was inhibited by molybdate, Tor-type DMSO reductases (e.g., Rhodobacterales) increased. Vibrionales increased in relative abundance in both treatments, and metagenome assembled genomes (MAGs) affiliated to Vibrio had all genes encoding the subunits of DMSO reductases. Molar conversion ratios of <1.3 CH4 per added DMSO were accompanied by a predominance of the methylotrophic methanogens Methanosarcinales. Enrichment of mtsDH genes, encoding for DMS methyl transferases in metagenomes of batch incubations indicate their role in DMS-dependent methanogenesis. MAGs affiliated to Methanolobus carried the complete set of genes encoding for the enzymes in methylotrophic methanogenesis.

Efficient heterotrophic nitrification by a novel bacterium Sneathiella aquimaris 216LB-ZA1-12T isolated from aquaculture seawater.

High concentration of ammonia poses a common threat to the healthy breeding of marine aquaculture organisms. Since aquaculture water is rich in organic matter, heterotrophic nitrifying bacteria might play a crucial role in ammonia removal. However, their roles in ammonia oxidation remain unknown. Here, we report a novel strain isolated from shrimp aquaculture seawater, identified as Sneathiella aquimaris 216LB-ZA1-12T, capable of heterotrophic nitrification. It is the first characterized heterotrophic nitrifier of the order Sneathiellales in the class Alphaproteobacteria. It exhibits high activity in heterotrophic nitrification, removing nearly 94% of ammonium-N under carbon-constrained conditions in 8 days with no observed nitrite accumulation. The heterotrophic nitrification pathway, inferred based on detection and genomic data was as follows: NH4+→NH2OH→NO→NO2-→NO3-. While this pathway aligns with the classical nitrification pathway, while the significant difference lies in the absence of classical HAO and HOX encoding genes in the genome, which is common in heterotrophic nitrifying bacteria. In summary, this bacterium is not only valuable for studying the nitrifying mechanism, but also holds potential for practical applications in ammonia removal in marine aquaculture systems and saline wastewater.

A previously uncharacterized divisome-associated lipoprotein, DalA, is needed for normal cell division in Rhodobacterales.

The bacterial cell envelope is a key subcellular compartment with important roles in antibiotic resistance, nutrient acquisition, and cell morphology. We seek to gain a better understanding of proteins that contribute to the function of the cell envelope in Alphaproteobacteria. Using Rhodobacter sphaeroides, we show that a previously uncharacterized protein, RSP_1200, is an outer membrane (OM) lipoprotein that non-covalently binds peptidoglycan (PG). Using a fluorescently tagged version of this protein, we find that RSP_1200 undergoes a dynamic repositioning during the cell cycle and is enriched at the septum during cell division. We show that the position of RSP_1200 mirrors the location of FtsZ rings, leading us to propose that RSP_1200 is a newly identified component of the R. sphaeroides' divisome. Additional support for this hypothesis includes the co-precipitation of RSP_1200 with FtsZ, the Pal protein, and several predicted PG L,D-transpeptidases. We also find that a ∆RSP_1200 mutation leads to defects in cell division, sensitivity to PG-active antibiotics, and results in the formation of OM protrusions at the septum during cell division. Based on these results, we propose to name RSP_1200 DalA (for division-associated lipoprotein A) and postulate that DalA serves as a scaffold to position or modulate the activity of PG transpeptidases that are needed to form envelope invaginations during cell division. We find that DalA homologs are present in members of the Rhodobacterales order within Alphaproteobacteria. Therefore, we propose that further analysis of this and related proteins will increase our understanding of the macromolecular machinery and proteins that participate in cell division in Gram-negative bacteria. IMPORTANCE Multi-protein complexes of the bacterial cell envelope orchestrate key processes like growth, division, biofilm formation, antimicrobial resistance, and production of valuable compounds. The subunits of these protein complexes are well studied in some bacteria, and differences in their composition and function are linked to variations in cell envelope composition, shape, and proliferation. However, some envelope protein complex subunits have no known homologs across the bacterial phylogeny. We find that Rhodobacter sphaeroides RSP_1200 is a newly identified lipoprotein (DalA) and that loss of this protein causes defects in cell division and changes the sensitivity to compounds, affecting cell envelope synthesis and function. We find that DalA forms a complex with proteins needed for cell division, binds the cell envelope polymer peptidoglycan, and colocalizes with enzymes involved in the assembly of this macromolecule. The analysis of DalA provides new information on the cell division machinery in this and possibly other Alphaproteobacteria.

Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60.

Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.

Plant growth promoting rhizobacteria modulates the antioxidant defense and the expression of stress-responsive genes providing Pb accumulation and tolerance of grass pea.

To ensure the success of phytoremediation, it is important to consider the appropriate combination of plants and microorganisms. This study was conducted to get a better insight into the underlying molecular and biochemical mechanism of grass pea (Lathyrus sativus L.) induced by plant growth promoting rhizobacteria (PGPR), when exposed for 3, 6, 9, and 14 days to 1 mM Pb in a hydroponic system. The significant positive effect of bacterial inoculation was reproduced in various parameters. Results indicated that inoculation of PGPR significantly increased the accumulation of Pb by 20%, 66%, 43%, and 36% in roots and by 46%, 55%, 37%, and 46% in shoots, respectively after 3, 6, 9, and 14 days of metal exposure compared to the uninoculated plants. The metal accumulation in grass pea plants triggered a significant elevation in the synthesis of non-protein thiols (NPT), particularly in inoculated plant leaves where it was about 3 and 2-fold higher than the uninoculated set on the 6th and the 9th day. Nevertheless, Pb treatment significantly increased oxidative stress and membrane damage in leaves with the highest hydrogen peroxide (H2O2) production and tissue malondialdehyde (MDA) concentration recorded in uninoculated plants. Furthermore, the PGPR inoculation alleviated the oxidative stress, improved significantly plant tolerance, and modulated the activities of antioxidant enzymes (SOD, CAT, APX, GR, DHAR, and MDHAR). Similarly, the expression patterns of LsPCS, LsGCN, LsCNGC, LsGR, and LsGST through qRT-PCR demonstrated that bacterial inoculation significantly induced gene expression levels in leaves 6 days after Pb treatment, indicating that PGPR act as regulators of stress-responsive genes. The findings suggest the key role of PGPR (R. leguminosarum (M5) + Pseudomonas fluorescens (K23) + Luteibacter sp. + Variovorax sp.) in enhancing Pb accumulation, reducing metal toxicity, strengthening of the antioxidant system, and conferring higher Pb tolerance to grass pea plants. Hence, the association Lathyrus sativus-PGPR is an effective tool to achieve the goal of remediation of Pb contaminated sites.

Bioremediation of Heavy Metals by Rhizobacteria.

Heavy elements accumulate rapidly in the soil due to industrial activities and the industrial revolution, which significantly impact the morphology, physiology, and yield of crops. Heavy metal contamination will eventually affect the plant tolerance threshold and cause changes in the plant genome and genetic structure. Changes in the plant genome lead to changes in encoded proteins and protein sequences. Consuming these mutated products can seriously affect human and animal health. Bioremediation is a process that can be applied to reduce the adverse effects of heavy metals in the soil. In this regard, bioremediation using plant growth-promoting rhizobacteria (PGPRs) as beneficial living agents can help to neutralize the negative interaction between the plant and the heavy metals. PGPRs suppress the adverse effects of heavy metals and the negative interaction of plant-heavy elements by different mechanisms such as biological adsorption and entrapment of heavy elements in extracellular capsules, reduction of metal ion concentration, and formation of complexes with metal ions inside the cell.

Decoupling of respiration rates and abundance in marine prokaryoplankton.

The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.

Analysis of Blueberry Plant Rhizosphere Bacterial Diversity and Selection of Plant Growth Promoting Rhizobacteria.

Microbial metabolites in rhizosphere soil are important to plant growth. In this study, microbial diversity in blueberry plant rhizosphere soil was characterized using high-throughput amplicon sequencing technology. There were 11 bacterial phyla and three fungal phyla dominating in the soil. In addition, inorganic-phosphate-solubilizing bacteria (iPSB) in the rhizosphere soil were isolated and evaluated by molybdenum-antimony anti-coloration method. Their silicate solubilizing, auxin production, and nitrogen fixation capabilities were also determined. Eighteen iPSB in the rhizosphere soil strains were isolated and identified as Buttiauxella, Paraburkholderia and Pseudomonas. The higher phosphorus-solubilizing capacity and auxin production in blueberry rhizosphere belonged to genus Buttiauxella sp. The strains belong to genus Paraburkholderia had the same function of dissolving both phosphorus and producing auxin, as well as silicate and nitrogen fixation. The blueberry seeds incubated with the strains had higher germination rates. The results of this study could be helpful in developing the plant growth-promoting rhizobacteria (PGPR) method for enhancing soil nutrients to blueberry plant.

A microcosm approach for evaluating the microbial nonylphenol and butyltin biodegradation and bacterial community shifts in co-contaminated bottom sediments from the Gulf of Finland, the Baltic Sea.

Pollution of aquatic ecosystems with nonylphenol (NP) and butyltins (BuTs) is of great concern due to their effects on endocrine activity, toxicity to aquatic organisms, and extended persistence in sediments. The impact of contamination with NP and/or BuTs on the microbial community structure in marine sediments was investigated using microcosms and high-throughput sequencing. Sediment microcosms with NP (300 mg/kg) and/or BuTs (95 mg/kg) were constructed. Complete removal of monobutyltin (MBT) occurred in the microcosms after 240 days of incubation, while a residual NP rate was 40%. The content of toxic tributyltin (TBT) and dibutyltin (DBT) in the sediments did not change notably. Co-contamination of the sediments with NP and BuTs did not affect the processes of their degradation. The pollutants in the microcosms could have been biodegraded by autochthonous microorganisms. Significantly different and less diverse bacterial communities were observed in the contaminated sediments compared to non-contaminated control. Firmicutes and Gammaproteobacteria dominated in the NP treatment, Actinobacteria and Alphaproteobacteria in the BuT treatment, and Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Acidobacteria in the NP-BuT mixture treatment. The prevalence of microorganisms from the bacterial genera Halothiobacillus, Geothrix, Methanosarcina, Dyella, Parvibaculum, Pseudomonas, Proteiniclasticum, and bacteria affiliated with the order Rhizobiales may indicate their role in biodegradation of NP and BuTs in the co-contaminated sediments. This study can provide some new insights towards NP and BuT biodegradation and microbial ecology in NP-BuT co-contaminated environment.

Halophilic Martelella sp. AD-3 enhanced phenanthrene degradation in a bioaugmented activated sludge system through syntrophic interaction.

Polycyclic aromatic hydrocarbons (PAHs) are a group of common recalcitrant pollutant in industrial saline wastewater that raised significant concerns, whereas traditional activated sludge (AS) has limited tolerance to high salinity and PAHs toxicity, restricting its capacity to degrade PAHs. It is therefore urgent to develop a bioaugmented sludge (BS) system to aid in the effective degradation of these types of compounds under saline condition. In this study, a novel bioaugmentation strategy was developed by using halophilic Martelella sp. AD-3 for effectively augmented phenanthrene (PHE) degradation under 3% salinity. It was found that a 0.5∼1.5% (w/w) ratio of strain AD-3 to activated sludge was optimal for achieving high PHE degradation activity of the BS system with degradation rates reaching 2.2 mg⋅gVSS-1⋅h-1, nearly 25 times that of the AS system. Although 1-hydroxy-2-naphthoic acid (1H2N) was accumulated obviously, the mineralization of PHE was more complete in the BS system. Reads-based metagenomic coupled metatranscriptomic analysis revealed that the expression values of ndoB, encoding a dioxygenase associated with PHE ring-cleavage, was 5600-fold higher in the BS system than in the AS system. Metagenome assembly showed the members of the Corynebacterium and Alcaligenes genera were abundant in the strain AD-3 bioaugmented BS system with expression of 10.3±1.8% and 1.9±0.26%, respectively. Moreover, phdI and nahG accused for metabolism of 1H2N have been annotated in both above two genera. Degradation assays of intermediates of PHE confirmed that the activated sludge actually possessed considerable degradation capacity for downstream intermediates of PHE including 1H2N. The degradation capacity ratio of 1H2N to PHE was 87% in BS system, while it was 26% in strain AD-3. These results indicated that strain AD-3 contributed mainly in transforming PHE to 1H2N in BS system, while species in activated sludge utilized 1H2N as substrate to grow, thus establishing a syntrophic interaction with strain AD-3 and achieving the complete mineralization of PHE. Long-term continuous experiment confirmed a stable PHE removal efficiency of 93% and few 1H2N accumulation in BS SBR system. This study demonstrated an effective bioaugmented strategy for the bioremediation of saline wastewater containing PAHs.

Advances in Biochar and PGPR engineering system for hydrocarbon degradation: A promising strategy for environmental remediation.

In soil, polycyclic aromatic hydrocarbons (PAHs) have resulted in severe environmental deterioration, compromised soil characteristics, and negatively affect all life forms, including humans. Developing appropriate and effective clean-up technology is crucial in solving the contamination issues. The traditional methods to treat PHAs contaminated soil are less effective and not ecofriendly. Bioremediation, based on bioaugmentation and biostimulation approaches, is a promising strategy for remediating contaminated soil. The use of plant growth-promoting rhizobacteria (PGPR) as a bioaugmentation tool is an effective technique for treating hydrocarbon contaminated soil. Plant growth-promoting rhizobacteria (PGPR) are group of rhizospheric bacteria that colonize the roots of plants. Biochar is a carbon-rich residue, which acts as a source of nutrients, and is also a bio-stimulating candidate to enhance the activities of oil-degrading bacteria. The application of biochar as a nutrient source to bioremediate oil-contaminated soil is a promising approach for reducing PHA contamination. Biochar induces polyaromatic hydrocarbons (PAHs) immobilization and removes the contaminants by various methods such as ion exchange electrostatic attractions and volatilization. In comparison, PGPR produce multiple types of biosurfactants to enhance the adsorption of hydrocarbons and mineralize the hydrocarbons with the conversion to less toxic substances. During the last few decades, the use of PGPR and biochar in the bioremediation of hydrocarbons-contaminated soil has gained greater importance. Therefore, developing and applying a PGPR-biochar-based remediating system can help manage hazardous PAH contaminated soil. The goal of this review paper is to (i) provide an overview of the PGPR mechanism for degradation of hydrocarbons and (ii) discuss the contaminants absorbent by biochar and its characteristics (iii) critically discuss the combined effect of PGPR and biochar for degradation of hydrocarbons by decreasing their mobility and bioavailability. The present review focuses on techniques of bioaugmentation and biostimulation based on use of PGPR and biochar in remediating the oil-contaminated soil.

Lanthanide-Dependent Methanol Metabolism of a Proteobacteria-Dominated Community in a Light Lanthanide-Rich Deep Environment.

This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln3+)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by Alpha-, Beta-, and Gammaproteobacteria represented by the four orders Methylococcales, Nitrosomonadales, Rhizobiales, and Xanthomonadales. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with Nitrosomonadales and Rhizobiales, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.

Differential Localization and Functional Specialization of parS Centromere-Like Sites in repABC Replicons of Alphaproteobacteria.

Partitioning systems ensure the stable inheritance of bacterial low-copy-number replicons, such as chromosomes, chromids, and megaplasmids. These loci consist of two genes encoding partition proteins A and B, and at least one parS centromere-like sequence. In chromids and megaplasmids, partitioning systems are often located in the vicinity of replication systems. An extreme example of this co-localization are alphaproteobacterial repABC replicons, where the partition (repAB) and replication (repC) genes form a single operon, with parS sequences usually positioned in close proximity to these genes. In this study, we characterized a more complex repABC system found in Paracoccus aminophilus (Rhodobacterales) megaplasmid pAMI4 (438 kb). Besides the repABC operon with a single parS site, this replicon has a 2-kb non-coding locus positioned 11.5 kb downstream of repC, which contains three additional parS repeats (3parS). We demonstrated that 3parS is bound by partition protein B in vitro and is essential for proper pAMI4 partitioning in vivo. In search of similar loci, we conducted a comparative analysis of parS distribution in other repABC replicons. This revealed different patterns of parS localization in Rhodobacterales and Rhizobiales. However, in both these taxonomic orders, parS sites are almost always located inside or close to the repABC operon. No other 3parS-like loci were found in the closest relatives of pAMI4. Another evolutionarily-independent example of such a locus was identified as a conserved feature in chromosome 2 of Allorhizobium vitis and related replicons. IMPORTANCE The repABC replication/partitioning loci are widespread in extrachromosomal replicons of Alphaproteobacteria. They are evolutionarily diverse, subject to multi-layer self-regulation, and are responsible for the maintenance of different types of replicons, such as plasmids (e.g., Agrobacterium pTi and pRi tumorigenic and rhizogenic plasmids), megaplasmids (e.g., Sinorhizobium pSymA and pSymB) and essential chromids (e.g., secondary chromosomes of Agrobacterium, Brucella and Rhodobacter). In this study, we functionally analyzed an atypical partition-related component of repABC systems, the 3parS locus, found in the P. aminophilus megaplasmid pAMI4. We also identified parS centromere-like site distribution patterns in different groups of repABC replicons and found other unrelated 3parS-like loci, which had been overlooked. Our findings raise questions concerning the biological reasons for differential parS distribution, which may reflect variations in repABC operon regulation as well as different replication and partition modes of replicons belonging to the repABC family.

Helping plants to deal with heavy metal stress: the role of nanotechnology and plant growth promoting rhizobacteria in the process of phytoremediation.

Heavy metals (HMs) are not destroyable or degradable and persist in the environment for a long duration. Thus, eliminating and counteracting the HMs pollution of the soil environment is an urgent task to develop a safe and sustainable environment. Plants are in close contact with the soil and can play an important role in soil clean-up, and the process is known as phytoremediation. However, under HM contaminated conditions, plants suffer from several complications, like nutrient and mineral deficiencies, alteration of various physiological and biological processes, which reduces the plant's growth rate. On the other hand, the bioavailability of HMs is another factor for reduced phytoremediation, as most of the HMs are not bioavailable to plants for efficient phytoremediation. The altered plant growth and reduced bioavailability of HMs could be overcome and enhance the phytoremediation efficiency by incorporating either nanotechnology, i.e., nanoparticles (NPs) or plant growth promoting rhizobacteria (PGPR) along with phytoremediation. Single incorporation of NPs and PGPR might improve the growth rate in plants by enhancing nutrient availability and uptake and also by regulating plant growth regulators under HM contaminated conditions. However, there are certain limitations, like a high dose of NPs that might have toxic effects on plants. Thus, the combination of two techniques such as PGPR and NPs-based remediation can conquer the limitations of individual techniques and consequently enhance phytoremediation efficiency. Considering the negative impacts of HMs on the environment and living organisms, this review is aimed at highlighting the concept of phytoremediation, the single or combined integration of NPs and PGPR to help plants deal with HMs and their basic mechanisms involved in the process of phytoremediation. Additionally, the complications of using NPs and PGPR in the phytoremediation process are discussed to determine future research questions and this will assist to stimulate further research in this field and increase its effectiveness in practical application.

Rhizobacteria communities reshaped by red mud based passivators is vital for reducing soil Cd accumulation in edible amaranth.

Red mud (RM) was constantly reported to immobilize soil cadmium (Cd) and reduce Cd uptake by crops, but few studies investigated whether and how RM influenced rhizobacteria communities, which was a vital factor determining Cd bioavailability and plant growth. To address this concern, high-throughput sequencing and bioinformatics were used to analyze microbiological mechanisms underlying RM application reducing Cd accumulation in edible amaranth. Based on multiple statistical models (Detrended correspondence analysis, Bray-Curtis, weighted UniFrac, and Phylogenetic tree), this study found that RM reduced Cd content in plants not only through increasing rhizosphere soil pH, but by reshaping rhizobacteria communities. Special taxa (Alphaproteobacteria, Gammaproteobacteria, Actinobacteriota, and Gemmatimonadota) associated with growth promotion, anti-disease ability, and Cd resistance of plants preferentially colonized in the rhizosphere. Moreover, RM distinctly facilitated soil microbes' proliferation and microbial biofilm formation by up-regulating intracellular organic metabolism pathways and down-regulating cell motility metabolic pathways, and these microbial metabolites/microbial biofilm (e.g., organic acid, carbohydrates, proteins, S2-, and PO43-) and microbial cells immobilized rhizosphere soil Cd via the biosorption and chemical chelation. This study revealed an important role of reshaped rhizobacteria communities acting in reducing Cd content in plants after RM application.