Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary

Manipulating soil microbial community assembly by the cooperation of exogenous bacteria and biochar for establishing an efficient and healthy CH4 biofiltration system

Manipulating the methanotroph (MOB) composition and microbial diversity is a promising strategy to optimize the methane (CH4) biofiltration efficiency of an engineered landfill cover soil (LCS) system. Inoculating soil with exogenous MOB-rich bacteria and amending soil with biochar show strong manipulating potential, but how the two stimuli interactively shape the microbial community structure and diversity has not been clarified. Therefore, three types of soils with active CH4 activities, including paddy soil, river wetland soil, and LCS were selected for enriching MOB-dominated communities (abbreviated as B_PS, B_RWS, and B_LCS, respectively). They were then inoculated to LCS which was amended with two distinct biochar. Besides the aerobic CH4 oxidation efficiencies, the evolution of the three microbial communities during the MOB enrichment processes and their colonization in two-biochar amended LCS were obtained. During the MOB enriching, a lag phase in CH4 consumption was observed merely for B_LCS. Type II MOB Methylocystis was the primary MOB for both B_PS and B_LCS; while type I MOB dominated for B_RWS and the major species were altered by gas concentrations. Compared to biochar, a more critical role was demonstrated for the bacteria inoculation in determining the community diversity and function of LCS. Instead, biochar modified the community structures by mainly stimulating the dominant MOB but could induce stochastic processes in community assembly, possibly related to its inorganic nutrients. Particularly, combined with biochar advantages, the paddy soil-derived bacteria consortiums with diverse MOB species demonstrated the potent adaption to LCS niches, not only retaining the high CH4-oxidizing capacities but also shaping a community structure with more diverse soil function. The results provided new insights into the optimization of an engineered CH4-mitigation soil system by manipulating the soil microbiomes with the cooperation of exogenous bacteria and biochar.

Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps

Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation.

IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.

Oxic urban rivers as a potential source of atmospheric methane

Urban rivers play a vital role in global methane (CH₄) emissions. Previous studies have mainly focused on CH₄ concentrations in urban rivers with a large amount of organic sediment. However, to date, the CH₄ concentration in gravel-bed urban rivers with very little organic sediment has not been well documented. Here, we collected water samples from an oxic urban river (Xin'an River, China; annual mean dissolved oxygen concentration was 9.91 ± 1.99 mg L^-1) with a stony riverbed containing very little organic sediment. Dissolved CH₄ concentrations were measured using a membrane inlet mass spectrometer to investigate whether such rivers potentially act as an important source of atmospheric CH₄ and the corresponding potential drivers. The results showed that CH₄ was supersaturated at all sampling sites in the five sampling months. The mean CH₄ saturation ratio (ratio of river dissolved CH₄ concentration to the corresponding CH₄ concentration that is in equilibrium with the atmosphere) across all sampling sites in the five sampling months was 204 ± 257, suggesting that the Xin'an River had a large CH₄ emission potential. The CH₄ concentration was significantly higher in the downstream river than in the upstream river (p < 0.05), which suggested that human activities along the river greatly impacted the CH₄ level. Statistical analyses and incubation experiments indicated that algae can produce CH₄ under oxic conditions, which may contribute to the significantly higher CH₄ concentration in August 2020 (p < 0.001) when a severe algal bloom occurred. Furthermore, other factors, such as heavy rainfall events, dissolved organic carbon concentration, and water temperature, may also be vital factors affecting CH₄ concentration. Our study enhances the understanding of dissolved CH₄ dynamics in oxic urban rivers with very little organic sediment and further proposes feasible measures to control the CH₄ concentration in urban rivers.