Biology subjects

Gu, J.-D.

Publications and source records attributed to Gu, J.-D..

5 recordsLinked to original sources

bioRxiv2023

Novel Anammox Bacteria Discovered in the Untapped Subsurface Aquifers

Anaerobic ammonium-oxidation (anammox) reaction is a crucial microbial nitrogen (N) transformation process contributing to the global N cycling. The currently known anammox bacteria are affiliated with two families, the marine Ca. Scalinduaceae and the freshwater Ca. Brocadiaceae, in the Planctomycetes. Here we report a discovery of new groups of anammox bacteria consisting of two new orders, two new families, and six new genera within the class Candidatus Brocadiia, all from geochemically distinct aquifer systems. Up to 25 high-quality metagenome-assembled genomes (MAGs) equipped with the core anammox metabolisms were recovered from 13 metagenomic datasets of aquifers and dominated the anammox bacterial communities in distinct aquifers unexpectedly. The comparatively smaller genome size (< 2.6 Mb) and higher coding density (> 85%) likely confer the survival advantage of them by reducing the energy consumption in cell replication and maintenance to increase the nutrient acquisition efficiency in the typically oligotrophic aquifers. Overall, the highly diversity of novel anammox bacterial lineages in aquifer systems largely expands our knowledge of the taxonomic diversity of anammox bacteria and highlights their global importance in aquifer N cycling.

microbiology↗

bioRxiv2021

A mixed blessing of viruses in wastewater treatment plants

Activated sludge of wastewater treatment plants harbors a very high diversity of both microorganisms and viruses, wherein the latter control microbial dynamics and metabolisms by infection and lysis of cells. However, it remains poorly understood how viruses impact the biochemical processes of activated sludge, for example in terms of treatment efficiency and pollutant removal. Using metagenomic and metatranscriptomic deep sequencing, the present study recovered thousands of viral sequences from activated sludge samples of three conventional wastewater treatment plants. Gene-sharing network indicated that most of viruses could not be assigned to known viral genera, implying activated sludge as an underexplored reservoir for new viruses and viral diversity. in silico Predictions of virus-host linkages demonstrated that infected microbial hosts, mostly belonging to bacteria, were transcriptionally active and able to hydrolyze polymers including starches, celluloses, and proteins. Some viruses encode auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and sulfur cycling, and antibiotic resistance genes (ARGs) for resistance to multiple drugs. The former group of virus-encoded genes (i.e. AMGs) may enhance the biodegradation of contaminants like starches and celluloses, suggesting a positive role for viruses in strengthening the performance of activated sludge. However, the latter group (i.e. ARGs) would be disseminated to different microorganisms using viruses as gene shuttles, demonstrating the possibility for viruses to facilitate the spread of antibiotic resistance in the environment. Collectively, this study highlights the mixed blessing of viruses in wastewater treatment plants, and deciphers how they manipulate the biochemical processes in the activated sludge, with implications for both environmental protection and ecosystem security.

microbiology↗

bioRxiv2020

Environmental conditions and diffusion-limited microbial transfer drive specific microbial communities detected at different sections in oil-production reservoir with water-flooding

This study investigated the distribution of microbial communities in the oilfield production facilities of a water-flooding petroleum reservoir and the roles of environmental variation, microorganisms in injected water, and diffusion-limited microbial transfer in structuring the microbial communities. Similar bacterial communities were observed in surface water-injection facilities dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria. Distinct bacterial communities were observed in downhole of the water-injection wells dominated by Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia, and in the oil-production wells dominated by Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaeal taxa in the water-injection facilities, while the oil-production wells were predominated by Methanosaeta, Methanomethylovorans, and Methanocalculus. Energy, nucleotide, translation, and glycan biosynthesis metabolisms were more active in the downhole of the water-injection wells, while bacterial chemotaxis, biofilm formation, two-component system, and xenobiotic biodegradation was associated with the oil-production wells. The number of shared OTUs and its positive correlation with formation permeability revealed differential diffusion-limited microbial transfer in oil-production facilities. The overall results indicate that environmental variation and microorganisms in injected water are the determinants that structure microbial communities in water-injection facilities, and the determinants in oil-bearing strata are environmental variation and diffusion-limited microbial transfer. IMPORTANCEWater-flooding continually inoculates petroleum reservoirs with exogenous microorganisms, nutrients, and oxygen. However, how this process influences the subsurface microbial community of the whole production process remains unclear. In this study, we investigated the spatial distribution of microbial communities in the oilfield production facilities of a water-flooding petroleum reservoir, and comprehensively illustrate the roles of environmental variation, microorganisms in injected water, and diffusion-limited microbial transfer in structuring the microbial communities. The results advance fundamental understanding on petroleum reservoir ecosystems that subjected to anthropogenic perturbations during oil production processes.

microbiology↗

bioRxiv2019

Highly diverse Asgard archaea participate in organic matter degradation in coastal sediments

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes (MAGs) from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involving in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomic evidence showed that all known Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, in different ecological niches in sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.

microbiology↗

bioRxiv2018

Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

Asgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2 using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

microbiology↗