Assessment of Biological Contribution to Natural Recovery of Anthropized Freshwater Sediments From Argentina: Autochthonous Microbiome Structure and Functional Prediction

The biotechnological potential of the Chloroflexota phylum

In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.

Sequential oxidation-composting-phytoremediation treatment for the management of an oily sludge from petroleum refinery

Oily sludges are generated in large quantities in petroleum refinery wastewater treatment plants. Given their complex composition, they are classified as hazardous waste. Selecting a single treatment technique for their remediation is challenging. This work aims to assess the extent of composting followed by phytoremediation on an oily sludge from an API separator unit, pre-treated by chemical oxidation with alkaline activated persulfate (PS). 18% of total petroleum hydrocarbons (TPH) were determined by IR spectroscopy. The aliphatic hydrocarbon content was 4714 ± 250 ppm by GC-FID, and aromatics were not detectable, suggesting a high amount of non-chromatographable complex hydrocarbons. The density of generalist and hydrocarbon-degrading populations of the oily sludge estimated by quantitative polymerase chain reaction (qPCR) evidenced an autochthonous microbiota with hydrocarbon-degrading capacity. The oxidative treatment with PS removed 31% of the TPH determined by IR after 20 days. The significant reduction of the native bacterial community was counterbalanced by coupling a composting treatment. Co-composting the sludge with goat manure and oat straw produced, after a year, a 96% reduction in TPH content, regardless of the oxidative pretreatment. Organic matter transformation was evidenced by the decrease of dissolved organic carbon (DOC) and the variation in E4/E6 ratio. The matrices obtained of composting were used as substrates for phytoremediation for 4 months. Ryegrass seeds were planted in both PS-treated and untreated sludge substrates. The presence of the plant grown in the pre-oxidised and composted substrate resulted in a higher aerial biomass of ryegrass (67%), an increase in enzymatic activities, and higher concentration of DOC, although without evidence of additional dissipation of TPH. The dynamics of the bacterial communities of the different substrates generated during the biological treatment were analyzed by Illumina NovaSeq DNA sequencing of 16S rRNA amplicons. The findings mirrored a succession compatible with that described in contaminated matrices, but also in other non-contaminated ones. According to these findings, an organic matter transformation process occurred, which included the complex hydrocarbons of the oily sludge, resulting in an active substrate that promoted the retention of nutrients and water and provided the necessary support for plant development.

Microbial community structure and metabolic profile of anthropized freshwater tributary channels from La Plata River, Argentina, to develop sustainable remediation strategies

Microbial communities from freshwater sediments are involved in biogeochemical cycles and they can be modified by physical and chemical changes in the environment. Linking the microbial community structure (MCS) with physicochemistry of freshwater courses allows a better understanding of its ecology and can be useful to assess the ecological impact generated by human activity. The MCS of tributary channels from La Plata River affected by oil refinery (C, D, and E) and one also by urban discharges (C) was studied. For this purpose, 16S rRNA metabarcoding analysis, in silico metagenome functional prediction, and the hydrocarbon degradation potential (in silico predictions of hydrocarbon-degrading genes and their quantification by qPCR) of the MCS were studied. Principal coordinate analysis revealed that the MCS was different between sites, and it was not structured by the hydrocarbon content. Site C showed physicochemical characteristics, bacterial taxa, and an in silico functional prediction related to fermentative/heterotrophic metabolism. Site D, despite having higher concentration of hydrocarbon, presented autotrophic, syntrophic, and methanogenic pathways commonly involved in natural processes in anoxic sediments. Site E showed and intermediate autotrophic/heterotrophic behavior. The hydrocarbon degradation potential showed no positive correlation between the hydrocarbon-degrading genes quantified and predicted. The results suggest that the hydrocarbon concentration in the sites was not enough selection pressure to structure the bacterial community composition. Understanding which is the variable that structures the bacterial community composition is essential for monitoring and designing of sustainable management strategies for contaminated freshwater ecosystems.

Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers

The goal of the study was to investigate the changes in the gut microbiota during the advancement of gastric cancer (GC) and identify pertinent taxa associated with the disease. We used a public fecal amplicon gastric cancer dataset from the Sequence Retrieval Archive (SRA), of patients with GC, gastritis, and healthy individuals. We did sequence pre-processing, including quality filtering of the sequences. Then, we performed a diversity analysis, evaluating α- and β-diversity. Next, taxonomic composition analysis was performed and the relative abundances of different taxa at the phylum and genus levels were compared between GC, gastritis, and healthy controls. The obtained results were subsequently subjected to statistical validation. To conclude, metagenomic function prediction was carried out, followed by correlation analysis between the microbiota and KEGG pathways. α analysis revealed a significant difference between male and female categories, while β analysis demonstrated significant distinctions between GC, gastritis, and healthy controls, as well as between sexes within the GC and gastritis groups. The statistically confirmed taxonomic composition analysis highlighted the presence of the microbes Bacteroides and Veillonella. Furthermore, through metagenomic prediction analysis and correlation analysis with pathways, three taxa, namely Akkermansia, Gammaproteobacteria, and Veillonella, were identified as potential biomarkers for GC. Additionally, this study reports, for the first time, the presence of two bacteria, Desulfobacteriota and Synergistota, in GC, necessitating further investigation. Overall, this research sheds light on the potential involvement of gut microbiota in GC pathophysiology; however, additional studies are warranted to explore its functional significance.

Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments

Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.