Dark Carbon Research Articles

Dark Carbon Fixation Measurements in the East Sea (Sea of Japan)

The vertical distribution patterns of daily primary production and dark carbon fixation were investigated at three stations in the East/Japan Sea (hereafter East Sea), a semi-enclosed marginal sea in the northwest Pacific Ocean. Our results displayed consistent vertical patterns of daily primary production at two of the stations, while the third station exhibited a markedly different distribution pattern, highlighting localized variations in production dynamics. In contrast, dark carbon fixations displaying varying vertical patterns among the stations are not specific enough to have much meaning. Water column-integral values showed differences in the contribution of dark carbon fixation to total primary production, ranging from 4.5% to 27.1%. These variations may reflect environmental parameters such as nutrient concentrations. However, our study is limited by the lack of direct data on the microbial community structure and chemoautotrophic activities, which are crucial for a more comprehensive understanding of these patterns. Understanding the environmental drivers of dark carbon fixation is crucial for elucidating carbon cycling dynamics in the East Sea. Notably, dark carbon fixation could contribute up to one-third of primary production in the region as an additional source of newly produced organic matter, highlighting the need for further investigation into this previously overlooked process.

Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean

Proteins in the open ocean represent a significant source of organic matter, and their profiles reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.

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.

Active dark carbon fixation evidenced by 14C isotope assimilation and metagenomic data across the estuarine-coastal continuum

Estuaries, as important land-ocean transitional zones across the Earth's surface, are hotspots of microbially driven dark carbon fixation (DCF), yet understanding of DCF process remains limited across the estuarine-coastal continuum. This study explored DCF activities and associated chemoautotrophs along the estuarine and coastal environmental gradients, using radiocarbon labelling and molecular techniques. Significantly higher DCF rates were observed at middle- and high-salinity regions (0.65–2.31 and 0.66–2.82 mmol C m−2 d−1, respectively), compared to low-salinity zone (0.07–0.19 mmol C m−2 d−1). Metagenomic analysis revealed relatively stable DCF pathways along the estuarine-coastal continuum, primarily dominated by Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway. Nevertheless, chemoautotrophic communities driving DCF exhibited significant spatial variations. It is worth noting that although CBB cycle played an important role in DCF in estuarine sediments, WL pathway might play a more significant role, which has not been previously recognized. Overall, this study highlights that DCF activities coincide with the genetic potential of chemoautotrophy and the availability of reductive substrates across the estuarine-coastal continuum, and provides an important scientific basis for accurate quantitative assessment of global estuarine carbon sink.

Dark carbon fixation in stream carbon cycling

AbstractHeadwater streams are often characterized by turbulence, organic matter inputs from terrestrial systems, net heterotrophy, and the microbial loop supplying carbon and energy for consumers. However, ecological models overlook dark carbon fixation (DCF), the light‐independent inorganic carbon uptake, mainly based on chemosynthesis, using energy yields from redox reactions. The quantification of microbial biomass production, including DCF, heterotrophic production (HP), gross primary production (GPP), and ecosystem respiration (ER) in lotic aquatic systems, has long yet to be addressed. Here, we investigate HP and DCF in water, sediment, and litter in addition to GPP and ER from streams in pristine rainforests in three distinct sub‐basins of the Amazon River, assessing the variety of turbid, black, and clear waters. We observed mean (min–max) values of microbial biomass production of about 0.1 (0.02–1.2), 3.2 (0.8–14.1), and 0.1 (0.02–0.5) mg C m−2 h−1 in water, sediment, and litter samples, in which DCF : HP showed mean (min–max) values of 0.5 (0.2–2), 0.02 (0.001–0.07), and 0.2 (0.001–0.5). Hence, measurements yielded DCF of similar magnitude as HP in water and litter but significantly lower in sediment, indicating that DCF supplied more carbon to planktonic and litter microbes than in top sediments of streams. Literature comparisons show similar DCF and GPP, both being lower than ER in streams. Finally, we found stream DCF higher than in lentic systems, suggesting that flow and turbulence may accelerate chemosynthesis.

Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.

Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.

High variability in organic carbon sources and microbial activities in the hadopelagic waters

AbstractHadal sediments are recognized as organic carbon depocenters with intensified microbial activity compared to adjacent abyssal sites due to focusing of relatively labile organic materials. However, the sources and turnover of hadopelagic organic carbon and its linkages to microbial activities have not been studied. We present the first synergic research on particulate organic carbon, dark carbon fixation, and size‐fractionated microbial community respiration proxy over the Atacama Trench. The results demonstrate that all parameters attenuate rapidly from surface to mesopelagic water (~ 1000 m). Progressing deeper, values remain relatively stable throughout bathypelagic (~ 4000 m) and abyssopelagic (~ 6000 m) waters. However, in the hadopelagic zone (> 6000 m), highly variable values indicate dynamic organic carbon sources and microbial activities in the deepest trench. On average, 71% of the microbial community respiration proxy is attributable to particle‐associated communities, indicating importance of particles for microbial metabolism. No apparent relationship was observed between the microbial community respiration proxy and microbial 16S rRNA gene abundance below the epipelagic depth, indicating variable supply and quality of organic carbon likely constrained heterotrophic activities rather than microbial abundances in the deep ocean. The depth‐integrated dark carbon fixation (> 1000 m) accounts for 11.5% ± 7.6% of the surface net primary production, of which 2.9% ± 0.4% is from hadopelagic depth. Dark carbon fixation is thus an important in situ organic carbon source for hadal life. This study suggests that high variability in organic carbon sources and microbial activities in the hadopelagic trench cannot be simply extrapolated from findings in the shallower dark ocean (e.g., 1000–6000 m).

Distinct Non-conservative Behavior of Dissolved Organic Matter after Mixing Solimões/Negro and Amazon/Tapajós River Waters.

Positive and negative electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and 1H NMR revealed major compositional and structural changes of dissolved organic matter (DOM) after mixing two sets of river waters in Amazon confluences: the Solimões and Negro Rivers (S + N) and the Amazon and Tapajós Rivers (A + T). We also studied the effects of water mixing ratios and incubation time on the composition and structure of DOM molecules. NMR spectra demonstrated large-scale structural transformations in the case of S + N mixing, with gain of pure and functionalized aliphatic units and loss of all other structures after 1d incubation. A + T mixing resulted in comparatively minor structural alterations, with a major gain of small aliphatic biomolecular binding motifs. Remarkably, structural alterations from mixing to 1d incubation were in essence reversed from 1d to 5d incubation for both S + N and A + T mixing experiments. Heterotrophic bacterial production (HBP) in endmembers S, N, and S + N mixtures remained near 0.03 μgC L-1 h-1, whereas HBP in A, T, and A + T were about five times higher. High rates of dark carbon fixation took place at S + N mixing in particular. In-depth biogeochemical characterization revealed major distinctions between DOM biogeochemical changes and temporal evolution at these key confluence sites within the Amazon basin.

Different behaviors of organic matter under physical-biological controls in the eastern Indian Ocean

Marine organic matter (OM) pools are the key to understanding biogeochemical cycles and carbon storage, especially under ongoing ocean warming. The tropical eastern Indian Ocean (IO) is ideal for unraveling marine OM pools for being one of the least understood ocean basins in terms of its complex physical and biogeochemical dynamics. So far, OM transformation and export remain underexplored and enigmatic in the IO. Here, we integrated in situ observations and incubation experiments in the Central IO (CIO) and Bay of Bengal (BoB). A large OM pool was found in the CIO, where we emphasized the prominent contribution of production in the deep euphotic layer, with physical forcing seasonally playing a supporting role. The dissolved organic matter (DOM)-degradation experiment results revealed high efficiency of in situ DOM consumption in the BoB, whereas dark carbon fixation by ammonia-oxidizing microorganisms was considered an alternative strategy in the euphotic CIO. Water mixing was found to highly influence the OM pools in the mesopelagic waters in the tropical eastern IO, but active microbial respiration could also regulate the OM degradation in the CIO. Our results emphasized the heterogeneity of OM pools between the BoB and CIO, and stated their different regulators of carbon reservoir considering an ocean warming scenario.

Potential response of dark carbon fixation to global warming in estuarine and coastal waters.

Dark carbon fixation (DCF), through which chemoautotrophs convert inorganic carbon to organic carbon, is recognized as a vital process of global carbon biogeochemical cycle. However, little is known about the response of DCF processes in estuarine and coastal waters to global warming. Using radiocarbon labelling method, the effects of temperature on the activity of chemoautotrophs were investigated in benthic water of the Yangtze estuarine and coastal areas. A dome-shaped thermal response pattern was observed for DCF rates (i.e., reduced rates at lower or higher temperatures), with the optimum temperature (Topt ) varying from about 21.9 to 32.0°C. Offshore sites showed lower Topt values and were more vulnerable to global warming compared with nearshore sites. Based on temperature seasonality of the study area, it was estimated that warming would accelerate DCF rate in winter and spring but inhibit DCF activity in summer and fall. However, at an annual scale, warming showed an overall promoting effect on DCF rates. Metagenomic analysis revealed that the dominant chemoautotrophic carbon fixation pathways in the nearshore area were Calvin-Benson-Bassham (CBB) cycle, while the offshore sites were co-dominated by CBB and 3-hydroxypropionate/4-hydroxybutyrate cycles, which may explain the differential temperature response of DCF along the estuarine and coastal gradients. Our findings highlight the importance of incorporating DCF thermal response into biogeochemical models to accurately estimate the carbon sink potential of estuarine and coastal ecosystems in the context of global warming.

Unexpected Structural Effects on the Onset of Thermal Reactions of Aromatic Hydrocarbons

This work aims to study the reactivity of a broad range of aromatic hydrocarbons to better understand the reactivities of more complex hydrocarbon mixtures. A set of closed-system pyrolysis experiments were conducted on a diverse range of ∼30 polycyclic aromatic hydrocarbons (PAHs) at the thermal onset reaction temperature of 400 °C to understand structural effects on reactivities and shed light on the early events of thermal reaction mechanisms. Thermal transformations, including methyl transfer (alkylation/dealkylation), rearrangement, condensation, molecular growth, and other chemical transformations, are often indicated by dark carbon materials composed of complex mixtures. Thermal transformation was confirmed by phenomenological changes (color and solubility) and chemical analysis using nuclear magnetic resonance, thermogravimetric analysis, gas chromatography, and electron spin resonance. Unsubstituted PAHs (e.g., phenanthrene, anthracene, pyrene, chrysene, etc.) were unaffected by heating at this temperature, with the exception of tetracene and pentacene which readily transformed into dark and insoluble materials. The reactivity of these unsubstituted PAHs is consistent with aromaticity predicted by the Clar theory. On the contrary, most alkyl-substituted PAHs can be transformed into carbon materials at 400 °C; however, alkyl-substituted phenanthrenes (2,7-dimethyl, 2-ethyl, or 7-ethyl) and benzenes (xylenes and pentamethylbenzene) were unreactive. CH2-containing PAH molecules were unreactive if in a five-membered ring (e.g., fluorene and benzofluorene) but became reactive if in a six-membered ring (9,10-dihydroanthracene), likely as a result of aromatization of the latter. The reactivity of the aryl–aryl linkage depends upon the aromatic moieties to which it is connected. While it is unreactive when connecting phenyl groups, such as in p-terphenyl, it is reactive when connecting pyrenes, such as in 1,1′-bispyrene. These results were unexpected and challenge the conventional thinking about hydrocarbon reactivities. Explanations and possible hypotheses are proposed, but more questions remain unanswered to understand the structural effects on reactivities. These findings are conducive to the sustainable use of aromatic hydrocarbons for higher value carbon materials and relevant to numerous pyrolysis studies on oil shale kerogens, biomass, and waste plastics.

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.

Growth as a function of sea ice cover, light and temperature in the arctic/subarctic coralline C. compactum: A year-long in situ experiment in the high arctic

Long-term, high-resolution measurements of environmental variability are sparse in the High Arctic. In the absence of such data, we turn to proxies recorded in the layered skeletons of the long-lived crustose coralline algae Clathromorphum compactum. Annual growth banding in this alga is dependent on several factors that include temperature, light availability, nutrients, salinity, and calcium carbonate saturation state. It has been observed that growth slows during winter as sunlight reaching the seafloor diminishes due to decreased insolation and the build-up of sea-ice, such that the relationship between sea-ice cover extent and algal growth has allowed for reconstructions of relative sea-ice variability through time. However, recent laboratory work has shown that C. compactum continue growing in complete darkness (sea-ice cover). Therefore, a more complete understanding of algal growth is necessary for the refinement of the sea-ice proxy. Here, we present the results of a ~year-long in-situ growth and environmental monitoring experiment in Arctic Bay, Nunavut, Canada (~73°N) which addresses, for the first time in situ, the gaps in our understanding of growth over an annual cycle in the High Arctic. Algal growth was assessed on a quasi-monthly basis, where specimens were subsampled to quantify monthly extension in the context of ocean temperature and light availability. By measuring extension rate through time, we observed that the algae grew on average 72 µm yr-1, with ~54% of annual growth occurring during the sea-ice free summer months (June-September), ~25% during the winter months (November-April), and ~21% occurring during the transition months of May and October. Although winter growth slowed, we did not observe a consistent cessation of linear extension during low-or no-light months. We posit that substantial growth during the winter months at this latitude is most likely a consequence of the mobilization of stored energy (photosynthate) produced during the photosynthetically active summer months. However, we also discuss the possibility of low light-photosynthetic activity and/or dark carbon fixation, which could also facilitate extension through time. Overall, the novel growth model presented here has implications for the use of C. compactum growth for reconstructing the environment as well as for trace-element-based (typically Mg/Ca) algal chronologies.

Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench.

ABSTRACTThe unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis.IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.

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.

A crucial phase in plants - it's a gas, gas, gas!

A crucial phase in plants - it's a gas, gas, gas!

Contribution of chemoautotrophy and heterotrophy to the microbial carbon cycle in the Southwestern Atlantic Ocean

Dark carbon fixation (DCF) is a source of new and labile carbon in the deep ocean, while heterotrophic microbial production (HMP) promotes organic matter transfer through the microbial loop. Despite their ecological relevance, there is a scientific gap regarding the estimates of DCF and HMP in the Southwestern Atlantic Ocean. Thus, the aim of this study was to investigate the spatial distribution of DCF and HMP; their relevance to the ocean carbon cycle; their relationship with environmental parameters and amongst themselves on the upper slope of Santos Basin. The samples were collected at three different water depths and sediment layers aboard the R/V Alpha Crucis in November 2019. DCF and HMP rates were measured by 14C-bicarbonate and 3H-leucine incorporation, respectively, and incubated in the dark. In the water column, DCF rates varied from 1.51 x 101 to 3.24 x 102 µg C m-3 h-1, which were one to two orders of magnitude lower than the HMP rates, from 1.26 x 102 to 1.48 x 104 µg C m-3 h-1. In the sediments, the DCF ranged from 1.15 x 104 to 1.83 x 105 µg C m-3 h-1, while HMP was one to four orders of magnitude lower, 3.22 x 101 to 1.56 x 103 µ gC m-3 h-1. DCF rates were significantly higher in the sediments, due to a higher availability of energy sources than in the oligotrophic water above. The HMP had higher rates in the water column as it is deeply dependent on organic matter derived from photosynthesis. This is the first study to investigate DCF and HMP considering the water column and sediments of the Southwestern Atlantic Ocean, thus contributing to a better understanding of the microbial role in the marine carbon cycle and ecosystem functioning.

Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool

Marine sponges host a wide diversity of microorganisms, which have versatile modes of carbon and energy metabolism. In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that the main microbial carbon fixation pathways in sponges are the Calvin–Benson–Bassham cycle (energized by light in Cyanobacteria, by sulfur compounds in two orders of Gammaproteobacteria, and by a wide range of compounds in filamentous Tectomicrobia), the reductive tricarboxylic acid cycle (used by Nitrospirota), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (active in Thaumarchaeota). Further, we observed that some sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. The lithoheterotrophic lifestyle was widespread and CO oxidation is the main energy source for sponge lithoheterotrophs. We also suggest that the molybdenum-binding subunit of dehydrogenase (encoded by coxL) likely evolved to benefit also organoheterotrophs that utilize various organic substrates. Genomic potential does not necessarily inform on actual contribution of autotrophs to light and dark carbon budgets. Radioisotope assays highlight variability in the relative contributions of photo- and chemoautotrophs to the total carbon pool across different sponge species, emphasizing the importance of validating genomic potential with physiology experimentation.

Microbial perspective on the giant carbonate ridge Alpha Crucis (Southwestern Atlantic upper slope).

Deep-sea carbonate mounds can harbor a wide variety of heterotrophic and chemosynthetic microbial communities, providing biodiversity hotspots among the deep-sea benthic ecosystems. This study examined the bacterial and archaeal diversity and community structure in the water column and sediments associated with a recently described giant carbonate mound named Alpha Crucis Carbonate Ridge (ACCR), located in the Southwestern Atlantic Ocean. Because of the acoustic evidence of gas chimneys from a previous study, we further evaluated the chemosynthetic primary production through in situ-simulated dark carbon fixation rates. Pelagic microbial communities varied significantly with depth, showing a high abundance of photosynthetic groups in surface waters and taxa related to nitrification in intermediate and deep waters. The benthic communities from the top of the ACCR were very similar along with the sediment depth, while those from the base of the ACCR showed a clear stratification pattern, with members in the deep strata mainly related to anoxic and chemosynthetic ecosystems. Dark carbon fixation rates were of the same order of magnitude as those of deep-sea cold seeps and hydrothermal vents. Our study provides the first description of the ACCR microbiome and adds new information to help formulate and implement future conservation and management strategies for vulnerable marine ecosystems.

A source of isotopically light organic carbon in a low-pH anoxic marine zone

Geochemical and stable isotope measurements in the anoxic marine zone (AMZ) off northern Chile during periods of contrasting oceanographic conditions indicate that microbial processes mediating sulfur and nitrogen cycling exert a significant control on the carbonate chemistry (pH, AT, DIC and pCO2) of this region. Here we show that in 2015, a large isotopic fractionation between DIC and POC, a DIC and N deficit in AMZ waters indicate the predominance of in situ dark carbon fixation by sulfur-driven autotrophic denitrification in addition to anammox. In 2018, however, the fractionation between DIC and POC was significantly lower, while the total alkalinity increased in the low-pH AMZ core, suggesting a predominance of heterotrophic processes. An isotope mass-balance model demonstrates that variations in the rates of sulfur- and nitrogen-mediated carbon fixation in AMZ waters contribute ~7–35% of the POC exported to deeper waters. Thus, dark carbon fixation should be included in assessments of future changes in carbon cycling and carbonate chemistry due to AMZ expansion.