Dark carbon fixation and chemolithotrophic microbial community in surface sediments of the cascade reservoirs, Southwest China

Metabolic diversity and adaptation of carbon-fixing microorganisms in extreme glacial cryoconite

Understanding the diversity and functionality of carbon-fixing microorganisms in glacial ecosystems is crucial for elucidating carbon cycling processes in extreme environments. This study investigates the composition, diversity, and metabolic potential of carbon-fixing microorganisms in Tibetan cryoconite. Through metagenomic sequencing, we identified 13 carbon-fixing metagenome-assembled genomes spanning ten known and three unclassified genera. Deoxyribonucleic acid -stable isotope probing experiments with 13C-labeled sodium bicarbonate confirmed the metabolic activity of key genera, including Cyanobacteria (Microcoleus and Phormidesmis) and Proteobacteria (Rhizobacter and Rhodoferax). Our results reveal a diverse array of carbon fixation pathways, with the Calvin-Benson-Bassham cycle and 3-hydroxypropionate bicycle being the most prominent. In addition to photoautotrophic microorganisms, chemoautotrophic microorganisms also contribute to carbon fixation through mechanisms such as sulfur oxidation and atmospheric reducing gas utilization. The study highlights the adaptability of microbial communities to varying environmental conditions, including fluctuations in oxygen, light, and substrate availability. The findings underscore the complex interplay between carbon fixation pathways and environmental factors in cryoconite ecosystems. It also emphasizes the importance of exploring alternative carbon fixation pathways to gain a more comprehensive understanding of carbon cycling in these harsh and dynamic ecosystems.

SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas

Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.

Different effects of seasonal impoundment and land use change on microbiome in a tributary sediment of the three gorgers reservoir

Anthropogenic activities significantly impact river ecosystem nutrient fluxes and microbial metabolism. Here, we examined the seasonal and spatial variation of sediments physicochemical parameters and the associated microbiome in the Pengxi river, a representative tributary of Three Gorges Reservoir, in response to seasonal impoundment and land use change by human activities. Results revealed that seasonal impoundment and land use change enhanced total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) concentration in the sediment, but have different effects on sediment microbiome. Sediment microbiota showed higher similarity during the seasonal high-water level (HWL) in consecutive two years. The abundant phyla Acidobacteria, Gemmatimonadetes, Cyanobacteria, Actinobacteria and Planctomycetes significantly increased as water level increased. Along the changes in bacterial taxa, we also observed changes in predicted carbon fixation functions and nitrogen-related functions, including the significantly higher levels of Calvin cycle, 4HB/3HP cycle, 3HP cycle and assimilatory nitrate reduction, while significantly lower level of denitrification. Though land use change significantly increased TOC, TN and NH4+-N concentration, its effects on spatial variation of bacterial community composition and predicted functions was not significant. The finding indicates that TGR hydrologic changes and land use change have different influences on the carbon and nitrogen fluxes and their associated microbiome in TGR sediments. A focus of future research will be on assessing on carbon and nitrogen flux balance and the associated carbon and nitrogen microbial cycling in TGR sediment.

Response of microbial communities and biogeochemical cycling functions to sediment physicochemical properties and microplastic pollution under damming and water diversion projects

Understanding the interactions among flow-sediment, microorganisms, and biogeochemical cycles is crucial for comprehending the ecological response mechanisms of dams and water diversion. This study focused on the spatial patterns of carbon, nitrogen, phosphorus, and sulfur (CNPS) cycle functional genes in the water resource for the middle route of the South-to-North Water Diversion Project in China, specifically the Danjiangkou Reservoir (comprising the Han and Dan reservoirs). The investigation incorporated sediment physicochemical properties and microplastic pollution. Numerous microbial species were identified, revealing that microbial communities demonstrated sensitivity to changes in sedimentary mud content. The communities exhibited greater β diversity due to finer sediment particles in the Han Reservoir (HR), whereas in the Dan Reservoir (DR), despite having higher sediment nutrient content and MPs pollution, did not display this pattern. Regarding the composition and structure of microbial communities, the study highlighted that sediment N and P content had a more significant influence compared to particle size and MPs. The quantitative microbial element cycling (QMEC) results confirmed the presence of extensive chemolithotrophic microbes and strong nitrogen cycle activity stemming from long-term water storage and diversion operations. The denitrification intensity in the HR surpassed that of the DR. Notably, near the pre-dam area, biological nitrogen fixation, phosphorus removal, and sulfur reduction exhibited noticeable increases. Dam construction refined sediment, fostering the growth of different biogeochemical cycling bacteria and increasing the abundance of CNPS cycling genes. Furthermore, the presence of MPs exhibited a positive correlation with S cycling genes and a negative correlation with C and N cycling genes. These findings suggest that variations in flow-sediment dynamics and MPs pollution have significant impact the biogeochemical cycle of the reservoir.

Metabolic adaptations underpin high productivity rates in relict subsurface water

Groundwater aquifers are ecological hotspots with diverse microbes essential for biogeochemical cycles. Their ecophysiology has seldom been studied on a basin scale. In particular, our knowledge of chemosynthesis in the deep aquifers where temperatures reach 60 °C, is limited. Here, we investigated the diversity, activity, and metabolic potential of microbial communities from nine wells reaching ancient groundwater beneath Israel's Negev Desert, spanning two significant, deep (up to 1.5 km) aquifers, the Judea Group carbonate and Kurnub Group Nubian sandstone that contain fresh to brackish, hypoxic to anoxic water. We estimated chemosynthetic productivity rates ranging from 0.55 ± 0.06 to 0.82 ± 0.07 µg C L-1 d-1 (mean ± SD), suggesting that aquifer productivity may be underestimated. We showed that 60% of MAGs harbored genes for autotrophic pathways, mainly the Calvin-Benson-Bassham cycle and the Wood-Ljungdahl pathway, indicating a substantial chemosynthetic capacity within these microbial communities. We emphasize the potential metabolic versatility in the deep subsurface, enabling efficient carbon and energy use. This study set a precedent for global aquifer exploration, like the Nubian Sandstone Aquifer System in the Arabian and Western Deserts, and reconsiders their role as carbon sinks.

Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

Four years of climate warming reduced dark carbon fixation in coastal wetlands

Dark carbon fixation (DCF), conducted mainly by chemoautotrophs, contributes greatly to primary production and the global carbon budget. Understanding the response of DCF process to climate warming in coastal wetlands is of great significance for model optimization and climate change prediction. Here, based on a 4-yr field warming experiment (average annual temperature increase of 1.5°C), DCF rates were observed to be significantly inhibited by warming in coastal wetlands (average annual DCF decline of 21.6%, and estimated annual loss of 0.08-1.5 Tg C yr-1 in global coastal marshes), thus causing a positive climate feedback. Under climate warming, chemoautotrophic microbial abundance and biodiversity, which were jointly affected by environmental changes such as soil organic carbon and water content, were recognized as significant drivers directly affecting DCF rates. Metagenomic analysis further revealed that climate warming may alter the pattern of DCF carbon sequestration pathways in coastal wetlands, increasing the relative importance of the 3-hydroxypropionate/4-hydroxybutyrate cycle, whereas the relative importance of the dominant chemoautotrophic carbon fixation pathways (Calvin-Benson-Bassham cycle and W-L pathway) may decrease due to warming stress. Collectively, our work uncovers the feedback mechanism of microbially mediated DCF to climate warming in coastal wetlands, and emphasizes a decrease in carbon sequestration through DCF activities in this globally important ecosystem under a warming climate.

Clay-associated microbial communities and their relevance for a nuclear waste repository in the Opalinus Clay rock formation

Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site-specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland. We found that the Opalinus Clay formation is mainly colonized by Alphaproteobacteria, Firmicutes, and Bacteroidota, which are known for corrosive biofilm formation. Potential iron-reducing bacteria were predominant in comparison to methanogenic archaea and sulfate-reducing bacteria. Despite microbial communities in Opalinus Clay being in majority homogenous, site-specific mineralogy and geochemistry conditions have selected for subcommunities that display metabolic potential for mineral dissolution and transformation. Our findings indicate that the presence of a potentially low-active mineral-associated microbial community must be further studied to prevent effects on the repository's integrity over the long term.

Microbial carbon fixation and its influencing factors in saline lake water

Microbial carbon fixation in saline lakes constitutes an important part of the global lacustrine carbon budget. However, the microbial inorganic carbon uptake rates in saline lake water and its influencing factors are still not fully understood. Here, we studied in situ microbial carbon uptake rates under light-dependent and dark conditions in the saline water of Qinghai Lake using a carbon isotopic labeling (¹⁴C-bicarbonate) technique, followed by geochemical and microbial analyses. The results showed that the light-dependent inorganic carbon uptake rates were 135.17-293.02 μg C L^-1 h^-1 during the summer cruise, while dark inorganic carbon uptake rates ranged from 4.27 to 14.10 μg C L^-1 h^-1. Photoautotrophic prokaryotes and algae (e.g. Oxyphotobacteria, Chlorophyta, Cryptophyta and Ochrophyta) may be the major contributors to light-dependent carbon fixation processes. Microbial inorganic carbon uptake rates were mainly influenced by the level of nutrients (e.g., ammonium, dissolved inorganic carbon, dissolved organic carbon, total nitrogen), with dissolved inorganic carbon content being predominant. Environmental and microbial factors jointly regulate the total, light-dependent and dark inorganic carbon uptake rates in the studied saline lake water. In summary, microbial light-dependent and dark carbon fixation processes are active and contribute significantly to carbon sequestration in saline lake water. Therefore, more attention should be given to microbial carbon fixation and its response to climate and environmental changes of the lake carbon cycle in the context of climate change.

Insights into autotrophic carbon fixation strategies through metagonomics in the sediments of seagrass beds

Seagrass beds contributes up to 10% ocean carbon storage. Carbon fixation in seagrass bed greatly affect global carbon cycle. Currently, six carbon fixation pathways are widely studied: Calvin, reductive tricarboxylic acid (rTCA), Wood-Ljungdahl (WL), 3-hydroxypropionate (3HP), 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) and dicarboxylate/4-hydroxybutyrate (DC/4-HB). Despite the knowledges about carbon fixation increase, the carbon fixation strategies in seagrass bed sediment remain unexplored. We collected seagrass bed sediment samples from three sites with different characteristics in Weihai, a city in Shandong, China. The carbon fixation strategies were investigated through metagenomics. The results exhibited that five pathways were present, of which Calvin and WL were the most dominant. The community structure of microorganisms containing the key genes of these pathways were further analyzed, and those dominant microorganisms with carbon fixing potential were revealed. Phosphorus significantly negatively corelated with those microorganisms. This study provides an insight into the strategies of carbon fixation in seagrass bed sediments.

Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load

Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.

Microbial ecology of the Southern Ocean

The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.

Anthropogenic regulation governs nutrient cycling and biological succession in hydropower reservoirs

Hydropower plays an important role in the supply of renewable energy, but it also exerts a great influence on the river continuum. Understanding nutrient cycling and microbial community succession in hydropower reservoirs is key to weighing hydroelectric pros and cons. However, the underlying control mechanisms are still not well known, especially with respect to the impacts of hydrological conditions. Based on a comprehensive survey of hydropower reservoirs along the Wujiang River in SW China and an integration of published data, we found that reservoir physicochemical and biological stratifications and planktonic microbial community assembly were synergistically evolving, and reservoir hydraulic load (i.e., mean water depth per unit retention time) was a key factor controlling the strength of stratifications, CO₂ and N₂O fluxes, nutrient retention efficiency, and bacterioplankton diversity. Hydraulic loads are artificially designed for hydropower reservoirs, and nutrient cycling and biological succession in reservoirs are thus governed by anthropogenic regulation. This study provides a theoretical basis to mitigate the environmental impacts of hydropower dams by regulating reservoir hydraulic load.

Dark carbon fixation in intertidal sediments: Controlling factors and driving microorganisms

Dark carbon fixation (DCF) contributes approximately 0.77 Pg C y^-1 to oceanic primary production and the global carbon budget. It is estimated that nearly half of the DCF in marine sediments occurs in estuarine and coastal regions, but the environmental factors controlling DCF and the microorganisms responsible for its production remain under exploration. In this study, we investigated DCF rates and the active chemoautotrophic microorganisms in intertidal sediments of the Yangtze Estuary, using ¹⁴C-labeling and DNA-stable isotope probing (DNA-SIP) techniques. The measured DCF rates ranged from 0.27 to 3.37 mmol C m^-2 day^-1 in intertidal surface sediments. The rates of DCF were closely related to sediment sulfide content, demonstrating that the availability of reductive substrates may be the dominant factor controlling DCF in the intertidal sediments. A significant positive correlation was also observed between the DCF rates and abundance of the cbbM gene. DNA-stable isotope probing (DNA-SIP) results further confirmed that cbbM-harboring bacteria, rather than cbbL-harboring bacteria, played a dominant role in DCF in intertidal sediments. Phylogenetic analysis showed that the predominant cbbM-harboring bacteria were affiliated with Burkholderia, including Sulfuricella denitrificans, Sulfuriferula, Acidihalobacter, Thiobacillus, and Sulfurivermis fontis. Moreover, metagenome analyses indicated that most of the potential dark-carbon-fixing bacteria detected in intertidal sediments also harbor genes for sulfur oxidation, denitrification, or dissimilatory nitrate reduction to ammonium (DNRA), indicating that these chemoautotrophic microorganisms may play important roles in coupled carbon, nitrogen, and sulfur cycles. These results shed light on the ecological importance and the underlying mechanisms of the DCF process driven by chemoautotrophic microorganisms in intertidal wetlands.

Interaction and Assembly of Bacterial Communities in High-Latitude Coral Habitat Associated Seawater

Threatened by climate change and ocean warming, coral reef ecosystems have been shifting in geographic ranges toward a higher latitude area. The water-associated microbial communities and their potential role in primary production contribution are well studied in tropical coral reefs, but poorly defined in high-latitude coral habitats to date. In this study, amplicon sequencing of 16S rRNA and cbbL gene, co-occurrence network, and βNTI were used. The community structure of bacterial and carbon-fixation bacterial communities showed a significant difference between the center of coral, transitional, and non-coral area. Nitrite, DOC, pH, and coral coverage ratio significantly impacted the β-diversity of bacterial and carbon-fixation communities. The interaction of heterotrophs and autotrophic carbon-fixers was more complex in the bottom than in surface water. Carbon-fixers correlated with diverse heterotrophs in surface water but fewer lineages of heterotrophic taxa in the bottom. Bacterial community assembly showed an increase by deterministic process with decrease of coral coverage in bottom water, which may correlate with the gradient of nitrite and pH in the habitat. A deterministic process dominated the assembly of carbon-fixation bacterial community in surface water, while stochastic process dominated t the bottom. In conclusion, the structure and assembly of bacterial and carbon-fixer community were affected by multi-environmental variables in high-latitude coral habitat-associated seawater.

Activity and structure of methanogenic microbial communities in sediments of cascade hydropower reservoirs, Southwest China

Freshwater reservoirs are an important source of the greenhouse gas methane (CH₄). However, little is known about the activity and structure of microbial communities involved in methanogenic decomposition of sediment organic matter (SOM) in cascade hydropower reservoirs. In this study, we targeted on sediments of three cascade reservoirs in Wujiang River, Southwest China. Our results showed that the content of sediment organic carbon (SOC) was between 3% and 11%, and it's positively correlated with both C/N ratio and recalcitrant organic carbon content of SOM. Meanwhile, SOC content was positively correlated with CH₄ production rates but had no significant correlation with total CO₂ production rates of the sediments, when rates were normalized to sediment volume. Resultantly, the sediment anaerobic decomposition rates hardly significantly increase along with the SOC content. These results suggested that the terrestrial organic matter accumulated after damming stimulated CH₄ production from the reservoir sediments even though its decomposition rate was limited. Meantime, high throughput sequencing of 16S rRNA genes indicated that not only the hydrogenotrophic and acetoclastic, but also the methylotrophic methanogens (Methanomassiliicoccus) are abundant in the reservoir sediments. Moreover, metagenomic sequencing also suggested that methylotrophic methanogenesis are potentially important in the sediment of cascade reservoirs. Finally, the hydraulic residence time of the reservoir could be the key controlling factor of the structures of bacterial and archaeal communities as well as the CH₄ production rates of the reservoir sediments.

Bicarbonate uptake rates and diversity of RuBisCO genes in saline lake sediments

There is limited knowledge of microbial carbon fixation rate, and carbon-fixing microbial abundance and diversity in saline lakes. In this study, the inorganic carbon uptake rates and carbon-fixing microbial populations were investigated in the surface sediments of lakes with a full range of salinity from freshwater to salt saturation. The results showed that in the studied lakes light-dependent bicarbonate uptake contributed substantially (>70%) to total bicarbonate uptake, while the contribution of dark bicarbonate uptake (1.35-25.17%) cannot be ignored. The light-dependent bicarbonate uptake rates were significantly correlated with pH and turbidity, while dark bicarbonate uptake rates were significantly influenced by dissolved inorganic carbon, pH, temperature and salinity. Carbon-fixing microbial populations using the Calvin-Benson-Bassham pathway were widespread in the studied lakes, and they were dominated by the cbbL and cbbM gene types affiliated with Cyanobacteria and Proteobacteria, respectively. The cbbL and cbbM gene abundance and population structures were significantly affected by different environmental variables, with the cbbL and cbbM genes being negatively correlated with salinity and organic carbon concentration, respectively. In summary, this study improves our knowledge of the abundance, diversity and function of carbon-fixing microbial populations in the lakes with a full range of salinity.