Complete genome sequence of Paracoccus sp. strain AK26: Insights into multipartite genome architecture and methylotropy

The Effect of Larval Exposure to Heavy Metals on the Gut Microbiota Composition of Adult Anopheles arabiensis (Diptera: Culicidae)

Anopheles arabiensis is a highly adaptable member of the An. gambiae complex. Its flexible resting behaviour and diverse feeding habits make conventional vector control methods less effective in controlling this species. Another emerging challenge is its adaptation to breeding in polluted water, which impacts various life history traits relevant to epidemiology. The gut microbiota of mosquitoes play a crucial role in their life history, and the larval environment significantly influences the composition of this bacterial community. Consequently, adaptation to polluted breeding sites may alter the gut microbiota of adult mosquitoes. This study aimed to examine how larval exposure to metal pollution affects the gut microbial dynamics of An. arabiensis adults. Larvae of An. arabiensis were exposed to either cadmium chloride or copper nitrate, with larvae reared in untreated water serving as a control. Two laboratory strains (SENN: insecticide unselected, SENN-DDT: insecticide selected) and F1 larvae sourced from KwaZulu-Natal, South Africa, were exposed. The gut microbiota of the adults were sequenced using the Illumina Next Generation Sequencing platform and compared. Larval metal exposure affected alpha diversity, with a more marked difference in beta diversity. There was evidence of core microbiota shared between the untreated and metal-treated groups. Bacterial genera associated with metal tolerance were more prevalent in the metal-treated groups. Although larval metal exposure led to an increase in pesticide-degrading bacterial genera in the laboratory strains, this effect was not observed in the F1 population. In the F1 population, Plasmodium-protective bacterial genera were more abundant in the untreated group compared to the metal-treated group. This study therefore highlights the importance of considering the larval environment when searching for local bacterial symbionts for paratransgenesis interventions.

Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits

The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.

Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome

Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.

From formic acid to single-cell protein: genome-scale revealing the metabolic network of Paracoccus communis MA5

With the increase in population growth and environmental pollution, the daily protein supply is facing great challenges. Single-cell protein (SCP) produced by microorganism fermentation is a good alternative for substituting plant- and animal-derived proteins. In this study, Paracoccus communis MA5 isolated from soil previously demonstrated an excellent ability to synthesize SCP directly from sodium formate. To investigate the central metabolic network of formic acid assimilation and protein synthesis, genome-scale analyses were performed. Genomic analysis showed that complete tetrahydrofolate cycle-, serine cycle-, glycolytic pathway-, tricarboxylic acid (TCA) cycle- and nitrogen metabolism-relevant genes were annotated in the genome. These pathways play key roles in the conversion of formic acid into proteins. Transcriptional analysis showed that sodium formate stress could stimulate the metabolic pathway in response to environmental stress, but weaken the sulfur metabolic pathway to inhibit amino acid synthesis, resulting in a decrease in protein content (30% vs 44%). However, under culture conditions with ammonium sulfate, metabolic pathways associated with protein synthesis were accelerated, causing an increase in protein content (53% vs 44%); while the tetrahydrofolate cycle associated with formic acid assimilation was inhibited, causing a 62.5% decrease in growth rate (OD600: 0.21 vs 0.56). These results provide evidence of protein synthesis from sodium formate in strain MA5 at the gene level and lay a theoretical foundation for the optimization of fermentation systems using formic acid as a carbon source.

Harnessing taxonomically diverse and metabolically versatile genus Paracoccus for bioplastic synthesis and xenobiotic biodegradation

The genus Paracoccus represents a taxonomically diverse group comprising more than 80 novel species isolated from various pristine and polluted environments. The species are characterized as coccoid shaped Gram-negative bacteria with versatile metabolic attributes and classified as autotrophs, heterotrophs and/or methylotrophs. Present study highlights the up-to-date global taxonomic diversity and critically discusses the significance of genome analysis for identifying the genomic determinants related to functional attributes mainly bioplastic synthesis and biodegradation potential that makes these isolates commercially viable. The analysis accentuates polyphasic and genomic attributes of Paracoccus spp. which could be harnessed for commercial applications and emphasizes the need of integrating genome based computational analysis for evolutionary species and functional diversification. The work reflects on the underexplored genetic potential for bioplastic synthesis which can be harnessed using advanced genomic methods. It also underlines the degradation potential and possible use of naturally-occurring pollutant-degrading Paracoccus isolates for development of biodegradation system and efficient removal of contaminants. The work contemplates plausible use of such potent isolates to establish the plant-microbe interaction, contributing towards contaminated land reclamation. Overall; the work signifies need and application of genome analysis to identify and explore prospective potential of Paracoccus spp. for environmental application towards achieving sustainability.

Bioaugmentation improves the anaerobic co-digestion of cadmium-containing plant residues and cow manure

Phytoremediation causes a large quantity of phytoremediation residues rich in heavy metals (HMs). This kind of plant residue can be used as a substrate for anaerobic digestion (AD) to reduce the content of HM-containing biomass, but high concentrations of HMs will inhibit the digestion efficiency and reduce the conversion efficiency of plant residues. Bioaugmentation may be an effective method to improve the degradation efficiency and methane yield of plant residues rich in HMs. In this study, a cellulose-degrading anaerobic bacteria Paracoccus sp. Termed strain LZ-G1 was isolated from cow dung, which can degrade cellulose and simultaneously adsorb Cd²⁺. The Cd²⁺ (10 mg/L)-adsorbtion efficiency and cellulose (463.12 g/kg)-degradation rate were 65.1 % and 60.59 %, respectively. In addition, using the strain LZ-G1 bioaugmented Cd²⁺-containing plant residues and cow manure mixed AD system, the system's biogas and methane production significantly increased (98.97 % and 142.03 %, respectively). During the AD process, the strain LZ-G1 was successfully colonized in the digestion system. Furthermore, the microbial community analysis revealed that LZ-G1 bioaugmentation alleviates the toxicity of free Cd²⁺ to the microbial community in the AD system, regulates and restores the archaea genus dominant in the methanogenesis stage, and restores the relative abundance of dominant bacteria associated with biomass hydrolysis. The restoration of the microbial community increased the biogas yield and methane production rate. Thus, bioaugmentation provides an easy and a feasible method for the actual on-site treatment of HM-rich phytoremediation residues.

Bioremediation characteristics, influencing factors of dichlorodiphenyltrichloroethane (DDT) removal by using non-indigenous Paracoccus sp

The marine bacterium able to consume DDT as the nutrient source was isolated from sea water which was identified as Paracoccus sp. DDT-21 based on 16 S rDNA gene sequence and Gram negative rod, obligate aerobic, non-motile biochemical characteristics. The isolate can degrade over 80% of the DDT, at a concentration of 50 mg/L in MSM in 72 h. Time and pollutant (DDT) dependent growth studies indicated that the isolate Paracoccus sp., DDT-21 significantly degrade the DDT and tolerates under DDT stress up to 50 mg/L. The DDT degradation capability of the strain Paracoccus sp. DDT-21 was found to be 5 ˃ 10 ˃ 15 ˃ 25 ˃ 50 mg/L DDT. The high concentrations (75 and 100 mg/L) of DDT showed significant decrease in DDT degradation. The optimal DDT degradation (∼90.0%) was observed at 6 g/L of yeast extract, 6% of glucose in pH 7.0 at 35 °C with 72 h of incubation as constant. Furthermore, four metabolites were observed by GC-MS analysis such as, DDE, DDD, DDMU, and DDA. The obtained results indicate that the isolate Paracoccus sp. DDT-21 is a promising candidate for the removal and/or detoxification of DDT in the environment.

Phylogenomic Framework for Taxonomic Delineation of Paracoccus spp. and Exploration of Core-Pan Genome

The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Paracoccus genomes (n = 103) showed concordant clustering of strains across multi-gene marker set phylogenies (nMC = 0.08-0.14); as compared to 16S rDNA phylogeny (nMC = 0.37-0.42) suggesting robustness of multi gene phylogenies in drawing phylogenetic inferences. Functional gene content distribution across the genus showed that only 1.7% gene content constitutes the core genome highlighting the significance of extensive genomic variability in the evolution of Paracoccus spp. Further, genome metrics were used to validate characterized strains, identifying classification anomalies (n = 13), and based on this, genome derived taxonomic amendments were notified in present study. Conclusively, validated metric tools can be employed on whole genome sequences, including draft assemblies, for the assessment and assignment of uncharacterized strains and species level ascription of newly isolated Paracoccus strains in future.