Iron (oxyhydr)oxides shift the methanogenic community in deep sea methanic sediment - insights from long-term high-pressure incubations

Role of Fe and Mn in organo-mineral-microbe interactions: evidence of carbon stabilization and transformation of organic matter leading to carbon greenhouse gas emissions

Up to 90% of organic matter (OM) in soils and sediments are stabilized and protected against microbial decomposition through organo-mineral interactions, formation of soil aggregates, pH, and oxygen availability. In soils and sediment systems, OM is associated with mineral constituents promoting carbon persistence and sequestration of which iron (Fe) and manganese (Mn) are crucial components. Under anoxic condition, microbes couple the decomposition of OM to the oxidative/reductive transformation of Fe/Mn minerals leading to carbon greenhouse gas (C-GHG) emissions (i.e. CH4 and CO2). Although these organo-mineral-microbe interactions have been observed for decades, the bio-geochemical mechanisms governing the switch from OM stability toward OM degradation are not fully understood. Interest in this field have been growing steadily given the interest in global warming caused by OM decomposition leading to C-GHG emissions. This review emphasizes the dual role of Fe/Mn minerals in both OM stability and decomposition. Additionally, we synthesize the conceptual understanding of how Fe/Mn minerals govern OM dynamics and the resultant C-GHG emissions via microbial-mediated carbon transformation. We highlight the need for interdisciplinary research to better understand organo-Fe/Mn mineral-microbial interactions to develop management handles for climate mitigation strategies.

Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression

Archaeal methanogenesis is a dynamic process regulated by various cellular and environmental signals. However, understanding this regulation is technically challenging due to the difficulty of measuring gene expression dynamics in individual archaeal cells. Here, we develop a multi-round hybridization chain reaction (HCR)-assisted single-molecule fluorescence in situ hybridization (FISH) method to quantify the transcriptional dynamics of 12 genes involved in methanogenesis in individual cells of Methanococcoides orientis. Under optimal growth condition, most of these genes appear to be expressed in a temporal order matching metabolic reaction order. Interestingly, an important environmental factor, Fe(III), stimulates cellular methane production without upregulating methanogenic gene expression, likely through a Fenton-reaction-triggered mechanism. Through single-cell clustering and kinetic analyses, we associate these gene expression patterns to a dynamic mixture of distinct cellular states, potentially regulated by a set of shared factors. Our work provides a quantitative framework for uncovering the mechanisms of metabolic regulation in archaea.

Methanococcoides cohabitans sp. nov., a marine methylotrophic methanogen isolated from an anaerobic methane-oxidizing enrichment culture

Enrichment cultures of archaea and bacteria performing the anaerobic oxidation of methane (AOM) regularly contain persistent methanogens. Here, we isolated the marine methanogen Methanococcoides cohabitans sp. nov. strain LMO-2T from a long-term AOM enrichment culture from the Northern Gulf of Mexico. Strain LMO-2T is Gram-stain-negative, irregular 0.5-1 µm coccus without flagella. It utilizes a variety of methylated compounds including methanol, monomethylamine, dimethylamine and trimethylamine for growth and methanogenesis. However, it does not grow on formate, acetate, dimethyl sulphate, H2/CO2, betaine and choline. The optimal conditions for growth were observed within a temperature range of 30-35 °C, a pH range of 7.0-8.0 and a salinity range of 2-4% NaCl. Based on the similarity and phylogeny of the 16S rRNA gene and genomic sequence, strain LMO-2T is classified within the genus Methanococcoides. Among the isolated type strains of the genus, strain LMO-2T exhibited the highest 16S rRNA gene sequence identity with Methanococcoides vulcani SLH33T (99.4%). The digital DNA-DNA hybridization and average nucleotide identity based on genome sequence showed that strain LMO-2T shared the highest similarity with Methanococcoides orientis LMO-1T, with values of 27.3% and 83.4%, respectively. In conclusion, we isolated a methylotrophic methanogen from an AOM culture, and the isolated strain LMO-2T represented a novel species of the genus Methanococcoides, for which the name Methanococcoides cohabitans sp. nov. is proposed. The type strain is LMO-2T (=CGMCC 1.18051T=KCTC 25774T).

Mechanisms of well iron clogging in groundwater heat pump systems: Insights from video imaging, hydrogeochemical analysis, and geochemical modeling

Groundwater heat pump (GWHP) systems are increasingly popular as low-carbon and environmentally friendly technologies, but well clogging induced by iron remains a significant issue. This study investigated the clogging characteristics and biogeochemistry of three typical wells (pumping, injection, and observation wells) in an operating GWHP system using video imaging, sampling, and analysis of hydrogeochemical and microbial data. The results revealed that iron-induced well clogging is a complex process involving physical, chemical, and microbial factors. Pumping wells experience clogging due to water mixing with varying redox conditions, resulting in hematite-based iron oxide deposits. Injection wells exhibit higher clogging severity, with transformed oxidation and accumulation of reduced iron minerals at the solid-liquid interface, resulting in darker colored clogs with magnetite. Clogging in both extraction and injection wells is closely related to iron-rich aquifer sections, where severe clogging occurs. Shallow clogging due to iron oxide is limited and attributed to the oxidation of zero-valent iron in well casing material. Iron-oxidizing bacteria and iron-reducing bacteria were detected in the consolidated deposits of clogged wells, indicating their involvement in the clogging formation process. Moreover, a strong correlation was observed between the presence of nitrate-reducing bacteria in the water phase and the severity of clogging, suggesting a possible link between iron oxidation and nitrate reduction in the system. Geochemical modeling results further supported the observed clogging severity in GWHP systems and confirmed varying clogging mechanisms in different wells and depths. These findings contribute to the understanding of clogging in GWHP operations, aiding in robust water utilization and energy-saving efforts, and supporting global carbon reduction initiatives.

Cycling and persistence of iron-bound organic carbon in subseafloor sediments

Reactive iron (FeR) serves as an important sink of organic carbon (OC) in marine surface sediments, which preserves approximately 20% of total OC (TOC) as reactive iron-bound OC (FeR-OC). However, the fate of FeR-OC in subseafloor sediments and its availability to microorganisms, remain undetermined. Here, we reconstructed continuous FeR-OC records in two sediment cores of the northern South China Sea encompassing the suboxic to methanic biogeochemical zones and reaching a maximum age of ~100 kyr. The downcore FeR-OC contributes a relatively stable proportion of 13.3 ± 3.2% to TOC. However, distinctly lower values of less than 5% of TOC, accompanied by notable 13C depletion of FeR-OC, are observed in the sulfate-methane transition zone (SMTZ). FeR-OC is suggested to be remobilized by microbially mediated reductive dissolution of FeR and subsequently remineralized, the flux of which is 18-30% of the methane consumption in the SMTZ. The global reservoir of FeR-OC in microbially active Quaternary marine sediments could be 19-46 times the size of the atmospheric carbon pool. Thus, the FeR-OC pool may support subseafloor microorganisms and contribute to regulating Earth's carbon cycle.

Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment

Since nitrate nitrogen (NO3--N) input has proved an effective approach for the treatment of black and odorous river waterbody, it was controversial whether the total nitrogen concentration standard should be raised when the effluent from the sewage treatment plant is discharged into the polluted river. To reveal the effect of exogenous nitrate (NO3--N) on black odorous waterbody, sediments with different features from contaminated rivers were collected, and the changes of physical and chemical characteristics and microbial community structure in sediments before and after the addition of exogenous NO3--N were investigated. The results showed that after the input of NO3--N, reducing substances such as acid volatile sulfide (AVS) in the sediment decreased by 80 % on average, ferrous (Fe2+) decreased by 50 %, yet the changing trend of ammonia nitrogen (NH4+-N) in some sediment samples increased while others decreased. High-throughput sequencing results showed that the abundance of Thiobacillus at most sites increased significantly, becoming the dominant genus in the sediment, and the abundance of functional genes in the metabolome increased, such as soxA, soxX, soxY, soxZ. Network analysis showed that sediment microorganisms evolved from a single sulfur oxidation ecological function to diverse ecological functions, such as nitrogen cycle nirB, nirD, nirK, nosZ, and aerobic decomposition. In summary, inputting an appropriate amount of exogenous NO3--N is beneficial for restoring and maintaining the oxidation states of river sediment ecosystems.

Soil nitrogen content and key functional microorganisms influence the response of wetland anaerobic oxidation of methane to trivalent iron input

Trivalent iron (Fe³⁺)-dependent anaerobic oxidation of methane (Fe-AOM), which is mediated by metal-reducing bacteria, is widely recognized as a major sink for the greenhouse gas methane (CH₄), and is a key driver of the carbon (C) biogeochemical cycle. However, the effect of Fe³⁺ addition on AOM in the present investigation is still ambiguous, and the mechanism is vague. In this study, we investigated the mechanism of changes in AOM response to Fe³⁺ input at different wetlands by using laboratory incubation methods combined with molecular biology techniques. Results indicated that Fe³⁺ input did not always lead to promoted AOM rates, which may be mediated by complex environmental factors, while lower soil total nitrogen (TN) had a positive effect on the response of AOM subjected to Fe³⁺ input. Notably, the promoted response of AOM was regulated by higher soil microbial diversity, of which the Shannon index was a key indicator leading to variation in the AOM response. Additionally, several biomarkers, including Planctomycetota and Burkholderiaceae, were key microorganisms responsible for alterations in AOM response. Our results suggest that the capacity of Fe³⁺ cycling-mediated AOM may gradually decrease in light of increasing anthropogenic N and Fe inputs to global estuarine wetlands, while its reaction processes will become more complex and more strongly coupled with multiple environmental factors. This finding contributes to the enhanced understanding and prediction of the wetland CH₄-related C with Fe cycles, as well as provides theoretical support for the underlying mechanisms.