Biology subjects

Nweze, J. E.

Publications and source records attributed to Nweze, J. E..

4 recordsLinked to original sources

bioRxiv2026

Synergistic plant-microbe interactions drive the remediation of naphthenic acid fractional compounds in a constructed wetland mesocosm

Constructed wetland treatment systems (CWTSs) are promising options for treating oil-sands process-affected water (OSPW), which contains toxic naphthenic acid fraction compounds (NAFCs). However, the molecular mechanisms underlying NAFCs attenuation by plants and root microbes remain poorly resolved. In our previous mesocosm study, common cattail (Typha latifolia) increased NAFCs removal by 2.5-fold relative to unplanted controls with no significant effect on plant growth. Here, using RNA from the same experimental system, we applied metatranscriptomics to 40 root samples collected over 60 days to examine plant and active-microbial responses to OSPW exposure. The active-root-associated-microbial community was dominated by Pseudomonadota, which showed a slight increase with exposure to OSPW. Burkholderiales were the most active family, though their relative activity decreased in OSPW systems, where Flavobacteriaceae (Bacteroidota) activity increased. Clear microbial-community shifts were driven by time and OSPW exposure. Although 18 previously proposed microbial NAFC-degradation genes were not differentially expressed, 42 other genes with potential roles in NAFC or related organic compound degradation showed differential expression in OSPW-filled mesocosms. This activity was dominated by specific oxidoreductases from Burkholderiales and Rhizobiales. Crucially, host plant actively responded to OSPW, robustly up-regulating genes encoding oxidoreductases, transporters, and glycosyltransferases, some of which are related to xenobiotic stress and detoxification. Taken together, these results show coordinated plant and microbial transcriptional responses in a system where NAFC removal had already been measured chemically. They help explain the response of OSPW-exposed mesocosms, but the observed patterns likely reflect the broader OSPW mixture rather than NAFCs alone.

ecology↗

bioRxiv2025

Uncovering hidden phylo- and ecogenomic diversity of the widespread methanotrophic genus Methylobacter

The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterise the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulphur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognised species diversity within the Methylobacter genus, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.

microbiology↗

bioRxiv2025

Cultivation and genomic characterisation of novel methanogens from a desert biocrust

Methanogens are strictly anaerobic archaea capable of energy conservation by methane production, yet their presence in oxic and arid environments challenges existing paradigms. In this study, we enriched and genomically characterised seven methanogenic cultures from desert biocrusts, affiliated with the genera Methanobacterium, Methanosarcina, and Methanocella. Six of these new cultures represent new species. Nonetheless, phylogenomic analyses revealed close genetic relationships with organisms from anoxic environments, indicating the absence of an evolutionary distinction. Comparative genomics exposed diverse though non-unique repertories of antioxidant (e.g. catalase, superoxide dismutase and desulfoferrodoxin), and desiccation-resistance genes (including genes for maintaining osmotic pressure and repair of cell wall and membrane), with Methanobacterium spp. possessing the lowest gene abundance and diversity for oxygen and desiccation tolerance. Nevertheless, the occurrence of a Class I methanogen such as Methanobacterium in arid soils challenges the notion that members of this class are less oxygen tolerant than Class II. Pangenome analysis further uncovered unique genes enriched in membrane-associated functions and potentially non-functional stress-related genes. Via a global metagenomic survey, we find that methanogens are underdetected in dryland soils, likely due to sequencing depth limitations. Our findings highlight previously overlooked methanogen diversity and ecological plasticity in oxic and desiccated habitats, and emphasise the need for further studies to elucidate their survival strategies.

microbiology↗

bioRxiv2024

Cellulose fermentation by the gut microbiota is likely not essential for the nutrition of millipedes

Millipedes are thought to depend on their gut microbiome for processing plant-litter-cellulose through fermentation, similar to many other arthropods. However, this hypothesis lacks sufficient evidence. To investigate this, we disrupted the gut microbiota of juvenile Epibolus pulchripes (tropical, CH4-emitting) and Glomeris connexa (temperate, non-CH4-emitting) using chemical inhibitors and isotopic labelling. Feeding the millipedes sterile or antibiotics-treated litter notably reduced faecal production and microbial load without major impacts on survival or weight. Bacterial diversity remained similar, with Bacteroidota dominant in E. pulchripes and Pseudomonadota in G. connexa. Sodium-2-bromoethanesulfonate treatment halted CH4 emissions and reduced the faecal mcrA copies in E. pulchripes after 14 days, but emissions resumed after returning to normal feeding. Methanogens in the order Methanobacteriales and Methanomasscilliicoccales associated with protists were detected using Catalysed Reporter Deposition Fluorescence In situ Hybridization (CARD-FISH) on day 21, despite suppressed CH4-emission. Employing 13C-labeled leaf litter and RNA-SIP revealed a slow and gradual prokaryote labelling, indicating a significant density shift only by day 21. In addition to labelling of taxa from orders well-recognized for their role in (ligno)cellulose fermentation (e.g., Bacteroidales, Burkholderiales, and Enterobacterales), others, such as members of Desulfovibrionales were also labelled. Surprisingly, labelling of the fungal biomass was somewhat quicker. Our findings suggest that fermentation by the gut microbiota is likely not essential for the millipedes nutrition. ImportanceMillipedes (Diplopoda) constitute the third most significant group of detritivores after termites and earthworms, yet they have been comparatively understudied. Traditionally, it was believed that millipedes gain energy from fermenting cellulose using their gut microbiota, similar to wood-feeding termites, but this belief lacks evidence. This study used two model millipede species, Epibolus pulchripes (large, tropical, and methane emitter) and Glomeris connexa (small, temperate, and non-methane emitter) to test this belief. We used chemical manipulation experiments, stable isotope labelling, and DNA sequencing to comprehend the microbiotas role in the millipedes nutrition. The findings suggest that cellulose fermentation by the gut microbiota may not be essential for millipede nutrition; instead, bacteriovory and fungivory might be the dominant feeding strategies of millipedes.

microbiology↗