Biology subjects

Sui, W.

Publications and source records attributed to Sui, W..

5 recordsLinked to original sources

bioRxiv2026

Physiological trade-offs drive the archaeal dominance and carbon turnover in deep subsurface

Marine sediments host a vast deep biosphere, yet how microorganisms persist under severe energy limitation and govern long-term organic carbon (OC) preservation remains poorly understood. Here we show that archaea, primarily Bathyarchaeia, systematically displace bacteria with depth and form net growth zones across East China Sea shelf deep sediments. Multi-omics analyses and bioenergetic modelling reveal that this transition is driven by sustained archaeal metabolism of diverse recalcitrant OC compounds, and a physiological trade-off that prioritizes cellular maintenance over growth, minimizing mortality in deep sediments. This strategy triggers a fundamental shift in sedimentary carbon turnover: from rapid bacterial degradation of labile OC near the surface to persistent archaea-driven turnover of recalcitrant OC at depth. We estimate that Bathyarchaeia mediate [~]77% of total OC degradation after 1,000 years of burial, corresponding to [~]18% ([~]11.4 Pg C) of millennial OC degradation in global shelf sediments. These findings identify subsurface archaea as key microbial regulators of long-term OC preservation and reveal how physiological trade-offs sustain life and carbon turnover in the energy-limited deep biosphere.

microbiology↗

bioRxiv2025

Rapid ecosystem collapse and biofilter formation following seabed methane leakage

Globally, vast amounts of methane are trapped within subseafloor gas hydrates. Recent evidence suggests that climate- and human-induced perturbations can destabilize gas hydrates and trigger methane release, yet the response of deep-sea ecosystems to these changes remains poorly understood. Here we show multi-year in situ monitoring of seabed ecosystem following methane leakage induced by hydrate exploration activities. Within just two years, benthic microbial and eukaryotic diversity in the affected areas declined significantly, while microbial and macrofaunal abundance increased. Integrated geochemical and omics analyses reveal the rapid successional shift of seabed ecosystem to a novel chemosynthetic system. Aerobic methanotrophs (Methyloprofundus) co-established with unexpectedly fast growing anaerobic methanotrophic archaea (ANME-3), accompanied by a rapid recruitment of opportunistic polychaetes that bioirrigated the seabed to >50 cm depths. The active animal-microbe interactions sustained exceptionally high rates of methane oxidation that utilized diverse electron acceptors. We demonstrate that methane hydrate destabilization can trigger rapid collapse of native seabed ecosystem while driving the formation of an effective methane biofilter consuming this potent greenhouse gas much faster than previously estimated. Understanding seabed ecosystem response and feedback is critical for predicting benthic methane cycling under ongoing global change and for developing sustainable strategies for methane hydrate resource management.

ecology↗

bioRxiv2025

Development and validation of an ultra-low-cost, open source normothermic ex vivo organ perfusion platform

BackgroundNormothermic ex vivo organ perfusion (NEVOP) promises to catalyze organ preservation, therapeutic discovery, and organ-specific disease modeling. Existing technology platforms remain inaccessible for research due to restricted access to commercial organ perfusion devices, high costs of both devices and proprietary consumables, and steep technical learning curves. Additionally, the available technology is not optimized to perfuse smaller organs such as the kidney. MethodsTo overcome these barriers, a custom NEVOP circuit was developed using recycled, repurposed, and low-cost components. Porcine kidneys and autologous blood were used to iteratively optimize circuit design. A porcine kidney autotransplantation protocol was adapted to evaluate in vivo kidney function after ex vivo perfusion. To pilot the flexibility of this system as a multi-organ platform for ex vivo human biology, non-transplantable human donor kidney, spleen, and pancreas specimens were stably perfused using human blood products and analyzed. ResultsAn ultra low-cost NEVOP system engineered to perfuse porcine kidneys and diverse human organs (kidney, pancreas, and spleen) sustained viable organs for up to 24 hours with evidence of both function and viability. Key innovations included a parallel flow resistor to facilitate low-flow perfusion in non-heparinized organs and a containment bag with adjustable magnets to provide vascular stability and recycling of venous overflow. The circuit costs less than 1,500USD to construct, and porcine kidneys perfused for 24 hours on this platform demonstrated healthy in vivo function upon autotransplantation. ConclusionsCustom NEVOP platforms constitute novel and potentially transformative research platforms which use low-cost and readily available materials. Paired with access to non-transplantable research organs from altruistic donors, this model provides a road map for investigators to advance biomedical discovery and human ex vivo biology.

bioengineering↗

bioRxiv2024

Aerobic carbon metabolism modulates nitrite ammonifiers for inhibiting nitrogen loss as revealed by microcosm experiment of agricultural upland soil

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA), two divergent nitrogen metabolism pathways, share nitrite as a common intermediate during anaerobic reduction. However, these pathways influence the environment and soil nutrients differently. Unlike denitrification, which involves nitrogen loss through gaseous nitrogen emission and nitrate leaching, DNRA is beneficial for the conservation of nitrogen. Nevertheless, the key mechanism underlying the joint regulation of aerobic carbon metabolism to nitrite ammonifiers in soil is still unclear, although previous studies have reported factors such as carbon and oxygen can independently affect DNRA. Here, microcosm experiments with agricultural upland soil were conducted under different aeration conditions supplemented with labile carbon to analyze the process of anaerobic nitrogen metabolism. The results indicated that denitrification exclusively dominated nitrite reduction when the soil was directly placed in an anaerobic environment. Nonetheless, a significant increase in DNRA activity and the attenuation of denitrification were detected when the soil was incubated aerobically with the addition of glucose prior to anaerobic incubation. Specifically, up to 55.8% of nitrite reduction switched to nitrogen conservation mainly via DNRA under high-carbon conditions. Quantitative assays of the nrfA gene and metagenomic data revealed a significant increase in DNRA-related genes after aerobic carbon metabolism. Furthermore, nrfA gene sequence analysis revealed a significant shift in the composition of nitrite ammonifiers community. These results indicate that nitrate/nitrite metabolic flux in the soil could be regulated to enhance DNRA by stimulating facultative anaerobic nitrite ammonifiers such as Sedimentibacter under alternating aerobic and anaerobic environments with carbon metabolism. IMPORTANCEThis study revealed that aerobic conditions with a carbon supply strongly influence the community assembly of nitrite ammonifiers. Nitrite ammonifiers such as Sedimentibacter enriched under sufficient carbon and aeration conditions promoted the subsequent DNRA process under anaerobic conditions. Therefore, regulating the competition between DNRA and denitrification by altering functional microbiota would be a promising approach for improving the efficiency of fertilizer application and for reducing greenhouse gas emissions from denitrification. These findings are essential for understanding the biological mechanism of nitrogen cycling in dryland agricultural soil. Based on these findings, we may design a strategy to increase the abundance of nitrite ammonifiers in agricultural soil, which might promote DNRA metabolism to improve nitrogen retention. This strategy would ultimately enhance fertilizer use efficiency and mitigate the detrimental environmental effects of nitrogen fertilizer abuse.

microbiology↗

bioRxiv2020

Cross-feeding between Thauera aminoaromatica and Rhodococcus pyridinivorans drove quinoline biodegradation in a denitrifying bioreactor

The complex bacterial community is predominated by several taxa, such as Thauera and Rhodococcus, in a quinoline-degrading denitrifying bioreactor. Yet it remains unclear about how the interactions between the different bacteria mediate the quinoline metabolism in denitrifying condition. In this study, we designed a sequence-specific amplification to guide the isolation of the most predominant bacteria and obtained four strains of Thauera aminoaromatica, the representative of one key member in the bioreactor. Test on these isolates demonstrated that all of them were unable to strive on quinoline but could efficiently degrade 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing condition. However, another isolate, Rhodococcus pyridinivorans YF3, corresponding to the second abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 were largely varied with the quantity of available oxygen. Specifically, quinoline could only be converted into 2-hydroxyquinoline without further transformation under the condition with insufficient oxygen, e.g. less than 0.5% initial oxygen in the vials. However, if were aerobically pre-cultured in the medium with quinoline the resting cells of YF3 could anaerobically convert quinoline into 2-hydroxyquinoline. A two-strain consortium constructed with isolates from Thauera (R2) and Rhodococcus (YF3) demonstrated an efficient denitrifying degradation of quinoline. Thus, we experimentally proved that the metabolism interaction based on the 2-hydroxyquinoline cross-feeding between two predominant bacteria constituted the mainstream of quinoline degradation. This work sheds light on the understanding of mechanism of quinoline removal in the denitrifying bioreactor. ImportanceWe experimentally verified the most predominant Thauera sp. was indeed active degrader for the intermediate metabolites and the second abundant taxon Rhodococcus exerted, however, key function for opening the food box for a complex quinoline-degrading community. An ecological guild composed of two isolates was assembled, revealing the different roles of keystone organisms in the microbial community. This study, to our best knowledge, is the first report on the cross feeding between the initial attacker with unprofitable catalysis of reluctant heterocyclic compounds and the second bacterium which then completely degrade the compound transformed by the first bacterium. These results could be a significant step forward towards elucidation of microbial mechanism for quinoline denitrifying degradation.

microbiology↗