Degradation Of Aromatic Compounds Research Articles

Influence of olive cake dietary supplementation on fecal microbiota of dairy cows.

Olive by-products represent a valuable low-price feed supplement for animal nutrition. In the present study, the effect of the dietary destoned olive cake supplementation, on both composition and dynamics of the fecal bacterial biota of cow, was assessed by Illumina MiSeq analysis of the 16S rRNA gene. In addition, metabolic pathways were predicted by using the PICRUSt2 bioinformatic tool. Eighteen lactating cows, according to the body condition score, the days from calving, and the daily milk production were homogeneously allocated into two groups, control or experimental, and subjected to different dietary treatments. In detail, the experimental diet contained, along with the components of the control one, 8% of destoned olive cake. Metagenomics data revealed significant differences in abundance rather than in richness between the two groups. Results showed that Bacteroidota and Firmicutes were identified as the dominant phyla, accounting for over 90% of the total bacterial population. The Desulfobacterota phylum, able to reduce sulfur compounds, was detected only in fecal samples of cows allocated to the experimental diet whereas the Elusimicrobia phylum, a common endosymbiont or ectosymbiont of various flagellated protists, was detected only in cows subjected to the control diet. In addition, both Oscillospiraceae and Ruminococcaceae families were mainly found in the experimental group whereas fecal samples of control cows showed the presence of Rikenellaceae and Bacteroidaceae families, usually associated with the high roughage or low concentrate diet. Based on the PICRUSt2 bioinformatic tool, pathways related to carbohydrate, fatty acid, lipid, and amino acids biosynthesis were mainly up regulated in the experimental group. On the contrary, in the control group, the metabolic pathways detected with the highest occurrence were associated with amino acids biosynthesis and degradation, aromatic compounds degradation, nucleosides and nucleotides biosynthesis. Hence, the present study confirms that the destoned olive cake is a valuable feed supplement able to modulate the fecal microbiota of cows. Further studies will be conducted in order to deepen the inter-relationships between the GIT microbiota and the host.

Draft Genome Sequence of Bacillus thuringiensis SS2, from Dibenzofuran-Contaminated Soil, Reveals Putative Aromatic Compound Degradation Genes.

The draft genome sequence of strain Bacillus thuringiensis SS2 consists of 426 contigs assembled at the scaffold level, totaling 5,030,306 bp, and contains 5,288 putative PATRIC protein-coding genes, including genes responsible for total benzoate consumption, degradation of halogenated compounds, heavy metal tolerance/resistance, biosynthesis of secondary metabolites, and microcin C7 self-immunity protein.

Bacillus- and Lactobacillus-Based Dietary Synbiotics Are Associated with Shifts in the Oropharyngeal, Proximal Colonic, and Vaginal Microbiomes of Korean Native Black Pigs

In this study, we evaluated the modulatory effect of synbiotics (probiotics + prebiotics) on the oropharyngeal, proximal colonic, and vaginal microbiomes of Korean native pigs using 16S rRNA gene sequencing. We found increased abundances of an unclassified deltaproteobacterial genus in oropharyngeal communities of pigs supplemented with a Lactobacillus-based synbiotic. These pigs also had increased abundances of unclassified genera of Tremblayales and Lactobacillales in their proximal colons. In another group, pigs supplemented with a Bacillus-based synbiotic had increased Megasphaera and reduced Campylobacter within their oropharyngeal microbiota. In addition, their vaginal microbiota had increased Clostridium and Halalkalibacillus, as well as reduced Filifactor and Veillonella. We then explored changes in the predicted microbial functionality, associated with the synbiotics. Our analysis showed a reduction in the abundance of a fatty acid and lipid biosynthesis pathway among proximal colonic microbiomes of the Lactobacillus-fed pigs. In pigs supplemented with a Bacillus-based synbiotic, the analysis showed reduced pathway abundances for the biosynthesis of carbohydrates, as well as vitamins, cofactors, and carrier molecules within their oropharyngeal microbiomes. Meanwhile, their vaginal microbiomes had higher pathway abundances for aromatic compound degradation and secondary metabolite biosynthesis, but lower abundances for amino acid degradation. The results confirmed our hypothesis that dietary synbiotics modulate the microbiome, not only in the proximal colon, but also the oropharyngeal cavity and vaginal tract of these pigs.

Contrasting responses of cuticular bacteria of Pardosa pseudoannulata under cadmium stress

Although research into how spiders respond to cadmium (Cd)-induced toxicity is ongoing, little is known about the effects of Cd contamination on the exogenous microorganisms of spiders. The current study used 16 S rRNA gene sequencing to evaluate the richness and structure of external bacterial communities in the wolf spider Pardosa pseudoannulata under long- and short-term Cd stress. Our results showed that Proteobacteria and Acidibacter were the dominating bacterial phylum and genus. The alpha diversity analysis showed that the high background of Cd concentration (Cd) reduced bacterial alpha diversity, and short-term Cd (SCd) stress elevated bacterial richness and diversity. Hub bacterial genera, including Stenotrophobacter, Hymenobacter, Chitinophaga, and Bryobacter, were identified by co-occurrence network analysis and showed high connectance with other bacterial genera. Further investigation revealed 15 and 14 bacterial taxa that were classified distinctively under SCd and Cd stresses. Interestingly, functional prediction analysis showed that Cd stress enhanced some crucial pathways involved in specialized functions, including manganese oxidation and aromatic compound degradation. Random forest and correlation analyses found that the spider's molting time was the dominant driver affecting bacterial phyla (i.e., Proteobacteria and Planctomycetes) and genera (e.g., Acidibacter, Reyranella, and Haliangium). Collectively, this comprehensive analysis creates new perspectives to investigate the divergent responses of microbial communities in the spiders' external habitat under Cd stress, and provides valuable viewpoints for Cd pollution evaluation and control.

Comparison of the effects of probiotics, rifaximin, and lactulose in the treatment of minimal hepatic encephalopathy and gut microbiota.

Minimal hepatic encephalopathy (MHE) is an early stage in the pathogenesis of hepatic encephalopathy. Intestinal microbiota is involved in the pathogenesis of hepatic encephalopathy and has become an important therapeutic target. Since there is no unified treatment principle for MHE, this study was conducted to determine the safety and efficacy of different intestinal microecological modulators in the treatment of MHE, and to explore the potential mechanism through intestinal microbiota analysis. Patients with liver cirrhosis were screened for MHE using psychometric hepatic encephalopathy score test. Patients diagnosed with MHE were enrolled and received probiotics, rifaximin, or lactulose for 4 weeks. Adverse events were recorded. The psychometric hepatic encephalopathy score test was performed after treatment. Samples of blood and stool were collected at entry and 4 weeks. Blood samples were analyzed to assess blood ammonia, liver, kidney, and hemostatic functions. Stool microbiota were sequenced to confirm changes in microbial composition. Of 323 patients with liver cirrhosis, 74 patients were diagnosed with MHE. In all, 54 patients were enrolled and 52 who agree to follow-up were included in analysis. The recovery rates of MHE patients received probiotics, rifaximin, and lactulose were 58.8% (20/34), 45.5% (5/11), and 57.1% (4/7), respectively. Probiotics and rifaximin improved liver function in MHE patients to a certain extent. Taxonomic compositions of gut microbiota in MHE patients were distinct from healthy people before treatment; the differences were significantly reduced after treatment, and the gut microbiota gradually resembled the structure of healthy individuals. We found that the relative abundance of specific taxa associated with anti-inflammatory and good cognitive functions was increased in MHE patients after treatment. Accordingly, metabolic pathways in MHE patients were altered before and after treatment. Downregulated pathways after probiotics treatment included glycometabolism and degradation of aromatic compounds. After lactulose treatment, degradation pathways of arginine and ornithine showed a downward trend. Probiotics, rifaximin, and lactulose are safe and effective in the treatment of MHE, and improve the composition of gut microbiota to some extent.

Complete Genome Sequence of Gordonia polyisoprenivorans 135, a Promising Degrader of Aromatic Compounds

Gordonia polyisoprenivorans 135 is a promising degrader of aromatic hydrocarbons. It can utilize phenanthrene, anthracene, benzoate, chlorobenzoates, and phenol. The genome of strain 135 was completely sequenced; it consists of a single 5,988,360-bp circular chromosome (GC content of 67.01%).

Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes

BackgroundLipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at different timepoints of cultivation, and a differential gene expression analysis was performed between cells grown at a similar physiological situation.ResultsWe observed enhanced transcription of genes involved in oxidative phosphorylation and enzymes localized in mitochondria in CGHH compared to CG. Genes involved in protein turnover, including those encoding ribosomal proteins, translation elongation factors, and genes involved in building the proteasome also showed an enhanced transcription in CGHH compared to CG. At 10 h cultivation, another group of activated genes in CGHH was involved in β-oxidation, handling oxidative stress and degradation of xylose and aromatic compounds. Potential bypasses of the standard GUT1 and GUT2-glycerol assimilation pathway were also expressed and upregulated in CGHH 10 h. When the additional carbon sources from HH were completely consumed, at CGHH 36 h, their transcription decreased and NAD+-dependent glycerol-3-phosphate dehydrogenase was upregulated compared to CG 60 h, generating NADH instead of NADPH with glycerol catabolism. TPI1 was upregulated in CGHH compared to cells grown on CG in all physiological situations, potentially channeling the DHAP formed through glycerol catabolism into glycolysis. The highest number of upregulated genes encoding glycolytic enzymes was found after 36 h in CGHH, when all additional carbon sources were already consumed.ConclusionsWe suspect that the physiological reason for the accelerated glycerol assimilation and faster lipid production, was primarily the activation of enzymes that provide energy.

Draft Genome Sequence of Aspergillus ochraceus Strain DY1, a Lignin-Degrading Fungus Isolated from Wood Rot.

Aspergillus spp. are known for their lignin-degrading ability and also for the degradation of complex aromatic compounds. In this paper, we present the genome sequence of Aspergillus ochraceus strain DY1, which was isolated from rotten wood in a biodiversity park. The total genome size is 35,149,223 bp, including 13,910 hits of protein-encoding genes, with a GC content of 49.92%.

Microbiome of High-Rank Coal Reservoirs in the High-Production Areas of the Southern Qinshui Basin.

To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ13CDIC and TDS and lower SO42-, Fe3+ and NO3- concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO3- and SO42-, causing a decrease in the content of these two ions in the stagnant areas.

Optode-based chemical imaging of laboratory burned soil reveals millimeter-scale heterogeneous biogeochemical responses

Soil spatial responses to fire are unclear. Using optical chemical sensing with planar ‘optodes’, pH and dissolved O2 concentration were tracked spatially with a resolution of 360 μm per pixel for 72 h after burning soil in the laboratory with a butane torch (∼1300 °C) and then sprinkling water to simulate a postfire moisture event. Imaging data from planar optodes correlated with microbial activity (quantified via RNA transcripts). Post-fire and post-wetting, soil pH increased throughout the entire ∼13 cm × 17 cm × 20 cm rectangular cuboid of sandy loam soil. Dissolved O2 concentrations were not impacted until the application of water postfire. pH and dissolved O2 both negatively correlated (p < 0.05) with relative transcript expression for galactose metabolism, the degradation of aromatic compounds, sulfur metabolism, and narH. Additionally, dissolved O2 negatively correlated (p < 0.05) with the relative activity of carbon fixation pathways in Bacteria and Archaea, amoA/amoB, narG, nirK, and nosZ. nifH was not detected in any samples. Only amoB and amoC correlated with depth in soil (p < 0.05). Results demonstrate that postfire soils are spatially complex on a mm scale and that using optode-based chemical imaging as a chemical navigator for RNA transcript sampling is effective.

Enrichment of tetracycline-degrading bacterial consortia: Microbial community succession and degradation characteristics and mechanism

Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4−10) and at moderate/high temperatures (25–40 °C). Peptone with concentrations of 4–10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.

Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation.

Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.

Transcriptomic and Metabolomic Analyses of Palaemon carinicauda Hepatopancreas in Response to Enterocytozoon hepatopenaei (EHP) Infection

Enterocytozoon hepatopenaei (EHP), a microsporidian responsible for hepatopancreatic microsporidiosis, is a major pathogen in commercial shrimp production. Among the affected species, Palaemon carinicauda (formerly Exopalaemon carinicauda) is commercially important in China and represents a potential research model for studying crustaceans. However, little information is available on its response to EHP infection. Hence, this study analyzed the transcriptome and metabolome of P. carinicauda’s hepatopancreas using high-throughput sequencing and liquid chromatograph-mass spectrometry (LC-MS) to determine its response during the early stage of infection. The transcriptomic analyses identified 730 differentially expressed genes, of which those associated with EHP infection were enriched in metabolic pathways as well as detoxification and antioxidant pathways. In addition, 144 differential metabolites were identified using a combination of positive and negative ion modes in LC-MS. The Kyoto encyclopedia of genes and genomes pathway analyses further indicated that the degradation of aromatic compounds, the AMP-activated protein kinase signaling pathway and C5-branched dibasic acid metabolism were significantly enriched after EHP infection. These results could provide useful insights into the effects of EHP on shrimps during the early stages of infection and help to understand the mechanisms underlying the stunted growth of shrimps after infection.

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

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

Linking soil microbial community to the chemical composition of dissolved organic matter in a boreal forest during freeze–thaw cycles

Soil dissolved organic matter (DOM) is mainly derived from the microbial degradation of organic matter. Intense freeze–thaw cycles (FTCs) elicited by warming alter the production and consumption of DOM in boreal forest soils, but little is known about the interactions between soil microbial community and DOM chemical composition. In this study, a FTCs incubation experiment was conducted to investigate the association between DOM dynamics and microbial community. DOM fingerprints were characterized using pyrolysis gas chromatography-mass spectrometry (Py-GC/MS) technology, and bacterial and fungal community composition was analyzed using high-throughput sequencing and bioinformatics. Both two and six freeze–thaw cycles (2FTCs and 6FTCs) significantly increased soil dissolved organic carbon (DOC) and NH4+-N contents at 0–10 cm and 50–60 cm depths. FTCs significantly decreased the relative abundance of aromatic components in DOM, whereas increasing the relative abundance of polysaccharides and fatty acid methyl esters (FAMEs) in DOM. The degradation of lignin-derived aromatic compounds was accelerated and microbial-derived components accumulated. Also, bacterial community responded more sensitively to FTCs than fungal community. Significant changes in bacterial community network was observed during FTCs with increased linkages, shortened average path lengths, reduced modularity and relative abundance of dominant phyla, and decreased α diversity. However, FTCs only increased the average path length of soil fungal community. The higher connectivity indicated that FTCs enhanced the interactions between microbial community and DOM chemical components. FTCs led to a shift in bacterial keystone taxa from being present in specific DOM molecules to competing for common substrates. Overall, FTCs tended to activate DOM and increase availability, which could promote DOM turnover and increase soil C stabilization. These findings provide new insights into the molecular mechanisms of DOM dynamics in the boreal forest soils under increased FTCs.

Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid.

A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1Mb chromosome, a 2.7Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753T).

Pasture management intensification shifts the soil microbiome composition and ecosystem functions

Natural grasslands are important reservoirs of animal and plant biodiversity and provide several ecosystem services, through the action of soil microorganisms. The increased demand for food, energy, and cattle activity has led to the conversion of natural grasslands to cultivated systems. However, the consequences of this conversion for soil microbial diversity and ecosystem functioning are yet to be discovered. Here, we used the 16 S rRNA amplicon sequencing and a large set of soil and environmental variables to understand the possible effects of natural grasslands to cultivated pasture conversion on the soil microbial structure, composition, diversity, and functions. The study areas followed a gradient of increasing soil disturbance intensity, as follows: Natural grassland (NG), Improved-natural grassland (IG), Perennial-cultivated pasture (PP), and Annual-cultivated pasture (AP). Natural grassland conversion to managed and cultivated pastures decreased the abundances of Acidobacteria and Verrucomicrobia, while increased α-, γ-, and δ-Proteobacteria, Gemmatimonadetes, Bacteroidetes, Patescibacteria, and Latescibacteria. The predicted functional profiles have also changed, as functions like ‘cellulolytic and symbionts/parasites’ decreased after natural to cultivated pastures conversion, while ‘nitrogen respiration’, ‘sulfur respiration’, and ‘aromatic compound degradation’ functions increased. Aboveground plant diversity decrease influenced belowground microbial diversity. The main drivers of diversity, composition, and functional potential are associated with soil attributes affected by liming, like aluminum complexation. In conclusion, we have found taxonomic and functional differences between natural and managed grasslands (NG and IG, respectively) and cultivated pastures (PP and AP), with consequences for management strategies and biodiversity conservation priorities.

Evolving a New Electron Transfer Pathway for Nitrogen Fixation Uncovers an Electron Bifurcating-Like Enzyme Involved in Anaerobic Aromatic Compound Degradation.

Nitrogenase is the key enzyme involved in nitrogen fixation and uses low potential electrons delivered by ferredoxin (Fd) or flavodoxin (Fld) to reduce dinitrogen gas (N2) to produce ammonia, generating hydrogen gas (H2) as an obligate product of this activity. Although the phototrophic alphaproteobacterium Rhodopseudomonas palustris encodes multiple proteins that can reduce Fd, the FixABCX complex is the only one shown to support nitrogen fixation, and R. palustris Fix- mutants grow poorly under nitrogen-fixing conditions. To investigate how native electron transfer chains (ETCs) can be redirected toward nitrogen fixation, we leveraged the strong selective pressure of nitrogen limitation to isolate a suppressor of an R. palustris ΔfixC strain that grows under nitrogen-fixing conditions. We found two mutations were required to restore growth under nitrogen-fixing conditions in the absence of functional FixABCX. One mutation was in the gene encoding the primary Fd involved in nitrogen fixation, fer1, and the other mutation was in aadN, which encodes a homolog of NAD+-dependent Fd:NADPH oxidoreductase (Nfn). We present evidence that AadN plays a role in electron transfer to benzoyl coenzyme A reductase, the key enzyme involved in anaerobic aromatic compound degradation. Our data support a model where the ETC for anaerobic aromatic compound degradation was repurposed to support nitrogen fixation in the ΔfixC suppressor strain. IMPORTANCE There is increasing evidence that protein electron carriers like Fd evolved to form specific partnerships with select electron donors and acceptors to keep native electron transfer pathways insulated from one another. This makes it challenging to integrate a Fd-dependent pathway such as biological nitrogen fixation into non-nitrogen-fixing organisms and provide the high-energy reducing power needed to fix nitrogen. Here, we show that amino acid substitutions in an electron donor for anaerobic aromatic compound degradation and an Fd involved in nitrogen fixation enabled electron transfer to nitrogenase. This study provides a model system to understand electron transfer chain specificity and how new electron transfer pathways can be evolved for biotechnologically valuable pathways like nitrogen fixation.

Analyzing the Soil Microbial Characteristics of Poa alpigena Lindm. on Bird Island in Qinghai Lake Based on Metagenomics Analysis

Poa alpigena Lindm. is a dominant forage grass that is widely distributed on the Qinghai-Tibetan Plateau and is often used in the restoration of degraded grasslands. Soil microorganisms are major players in the cycling of materials in terrestrial ecosystems. In this study, based on high-throughput sequencing, the rhizosphere and non-rhizosphere soils of Poa alpigena L. on Bird Island, Qinghai Lake, were used to investigate the effects of Poa alpigena L. on the composition and structure of soil microbial communities, and to establish associated soil microbial gene pools. Results revealed that microorganisms in the soil of Poa alpigena L. on Bird Island belonged to 62 phyla, 112 classes, 245 orders, 518 families, 1610 genera, and 5704 species. The dominant soil bacteria in rhizosphere and non-rhizosphere soils were Proteobacteria (49.62%, 47.13%) and Actinobacteria (30.31% and 31.67%), whereas the dominant fungi were Ascomycota (3.15% and 3.37%) and Basidiomycota (0.98% and 1.06%). Alpha diversity analysis revealed that the microbial richness and diversity in non-rhizosphere soil were significantly higher than those in rhizosphere soil, mainly influenced by soil water content and total nitrogen content. Furthermore, on the basis of LEfSe analysis, Alphaproteobacteria and Betaproteobacteria were identified as prominent differential taxa for rhizosphere and non-rhizosphere soils, respectively. The key differential metabolic pathways of rhizosphere soil microorganisms were those associated with the ATP-binding cassette (ABC) transporter, basal metabolism, and cytochrome P450 metabolism, whereas those of non-rhizosphere soil microorganisms included the gene expression-related pathways, methane metabolism, and pathway associated with degradation of aromatic compounds. These findings indicated that the rhizosphere soil of Poa alpigena L. is selective for microorganisms that play important roles in the oxidation of methane and regulation of the greenhouse effect on Bird Island, and that the soil environment on this island may be subject to contamination with aromatic compounds.

Functional response of microbial communities in lab-controlled oil-contaminated marine sediment.

Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.