Niche differentiation of microbial community shapes vertical distribution of recalcitrant dissolved organic matter in deep-sea sediments

Marine Recalcitrant Dissolved Organic Matter Gained by Processing at Sandy Subterranean Estuaries

The sandy subterranean estuary (STE) connecting fresh groundwater to saline sea water is characterized by strong geochemical (salinity, redox, and pH) gradients, with evidence emerging for its role as a hot spot for consumption of labile substrates. This inspired us to conduct a study to evaluate whether this holds true for dissolved organic matter (DOM), especially given the still mysterious origin of marine recalcitrant DOM. Here, characterization of DOM of 21 groundwater samples (depth 1-13 m, salinity 3.9‰ to 32.4‰) across a 65 m transect of an STE located in coastal Guangdong, China, has found systematic biotransformation toward "recalcitrant" carboxyl-rich alicyclic molecules (CRAM). The fraction of CRAM (%CRAM) increases from 33.1% to 76.7% with an increasing degree of DOM degradation and increasing salinity. Further, processing of DOM, including the more "biolabile" DOM with lower %CRAM released from aquitard, is more active under oxic conditions than under reducing conditions. Given the large quantities of sea water that recirculates through the sandy STEs globally, the amount of "recalcitrant" DOM (RDOM) entering the ocean after processing is likely to be considerable. While more studies are needed, the ocean can gain "recalcitrant" CRAM-like compounds in this way.

Adaptation of Archaeal Communities to Summer Hypoxia in the Sediment of Bohai Sea

Understanding the adaptation of archaea to hypoxia is essential for deciphering the functions and mechanisms of microbes when suffering environmental changes. However, the dynamics and responses of archaea to the sedimentary hypoxia in Bohai Sea are still unclear. In this study, the diversity, composition, and distribution of archaeal community in sediment along an inshore-offshore transect across the oxygen-depleted area in the Bohai Sea were investigated in June, July, and August of 2021 by employing high-throughput sequencing of 16S rRNA gene. Results indicated that the archaeal communities were dominated by Thermoproteota (80.61%), Asgardarchaeota (8.70%), and Thermoplasmatota (5.27%). Dissolved oxygen (DO) and NO3 - were the two key factors shaping the distribution of archaeal communities, accounting for 49.5% and 38.3% of the total variabilities (p < 0.05), respectively. With the intensity of oxygen depletion, the diversity of archaeal communities increased significantly. Microbial networks revealed that Bathyarchaeia played a key role in interacting with both bacteria and other archaeal groups. Furthermore, adaptions to hypoxia of archaea were also displayed by variation in relative abundance of the predicted ecological functions and the metabolic pathways. The enrichment of specific nitrogen transformation enzymes showed the potential for nitrogen fixation and removal, which might contribute to the balance of N budget and thus facilitate the ecological restoration under eutrophication in Bohai Sea. Our results provided a new picture on ecological and metabolic adaptions to hypoxia by archaea, which will be beneficial to further investigations in extreme environments both theoretically and practically.

Chemodiversity of dissolved organic matter and its association with the bacterial community at a zinc smelting slag site after 10 years of direct revegetation

Dissolved organic matter (DOM) plays a critical role in driving the development of biogeochemical functions in revegetated metal smelting slag sites, laying a fundamental basis for their sustainable rehabilitation. However, the DOM composition at the molecular level and its interaction with the microbial community in such sites undergoing long-term direct revegetation remain poorly understood. This study investigated the chemodiversity of DOM and its association with the bacterial community in the rhizosphere and non-rhizosphere slags of four plant species (Arundo donax, Broussonetia papyrifera, Cryptomeria fortunei, and Robinia pseudoacacia) planted at a zinc smelting slag site for 10 years. The results indicated that the relative abundance of lipids decreased from 18 % to 5 %, while the relative abundance of tannins and lignins/CRAM-like substances increased from 4 % to 10 % and from 44 % to 64 % in the revegetated slags, respectively. The chemical stability of the organic matter in the rhizosphere slag increased due to the retention of recalcitrant DOM components, such as lignins, aromatics, and tannins. As the diversity and relative abundance of the bacterial community increased, particularly within the Proteobacteria, there was better utilization of recalcitrant components (e.g., lignins/CRAM-like compounds), but this utilization was not invariable. In addition, potential preference associations between specific bacterial OTUs and DOM molecules were observed, possibly stimulated by heavy metal bioavailability. Network analysis revealed complex connectivity and strong interactions between the bacterial community and DOM molecules. These specific interactions between DOM molecules and the bacterial community enable adaptation to the harsh conditions of the slag environment. Overall, these findings provide novel insights into the transformation of DOM chemodiversity at the molecular level at a zinc smelting slag sites undergoing long-term revegetation. This knowledge could serve as a crucial foundation for developing direct revegetation strategies for the sustainable rehabilitation of metal smelting slag sites.

Seaweed burial mitigated the release of organic carbon and nutrients by regulating microbial activity

Seaweed debris is susceptible to being buried in sediments due to natural environmental changes and human activities. So far, the effect of buried seaweeds on the environment and its decomposition mechanism remains unclear. This study simulated the decomposition of seaweed Gracilariopsis lemaneiformis for 180 days with different burial depths (0 cm and 10 cm) and burial weights (10 g and 20 g). Our findings revealed that compared with Gracilariopsis decomposition on the sediment surface, the seaweed buried in sediment slowed down the release of N, P, and dissolved organic carbon (DOC) by enhancing the activity of diverse anaerobic microbes (i.e. Draconibacterium, Desulfuromusa, Sediminispirochaeta), which were associated with organic matter decomposition. The enhanced burial quantity of Gracilariopsis resulted in a 3.28 % increase in sediment OC and enriched the humification degree of DOC in seawater. These results highlight the role of seaweed burial in enhancing OC sequestration in marine environments.

Stability of sedimentary organic matter: Insights from molecular and redox analyses

Sedimentary organic matter (SOM) affects the stability of the aquatic carbon pool. The degradation process of SOM is complex for its multifaceted composition. The concentration and properties of SOM affect its steady state, yet the transformation processes of SOM in lakes remain unclear. Here we show the molecular and redox perspectives of SOM stability in polluted sediments with high organic matter content and diverse vegetation. We find significant differences in carbon fractions across various sites. The origin of the organic matter, determined using excitation-emission matrix spectra, influences the consistency of organic matter composition and biochemical degradation in lacustrine sediment. We also observe that sulfur-containing substances decrease carbon chain length and reduce organic matter stability. Fourier-transform ion cyclotron resonance mass spectrometry shows that sulfur-containing substances decrease the degree of saturation and cause reduction. In contrast, nitrogen-containing compounds increase the modified aromaticity index and humin content, enhancing organic carbon complexity and stability (p < 0.05). These results complement the characteristics and transformations of SOM. In a broader perspective, this study contributes to laying the foundation for understanding SOM stability in the carbon cycle and its future effects.

The Process of Soil Carbon Sequestration in Different Ecological Zones of Qingtu Lake in the Arid-Semi-Arid Region of Western China

As a vital component of the global carbon pool, soils in arid and semi-arid regions play a significant role in carbon sequestration. In the context of global warming, increasing temperatures and moisture levels promote the transformation of barren land into wetlands, enhancing carbon sinks. However, the overdevelopment of oases and excessive extraction of groundwater lead to the opposite effect, reducing carbon sequestration. This study examines two soil types-meadow soil (MS) and swamp soil (SS)-from Qingtu Lake, an arid lake in western China. It analyzes the sources of soil inorganic carbon, the composition and origin of dissolved organic matter (DOM), and the relationships between microbes, soil organic carbon (SOC), soil inorganic carbon (SIC), mineral composition, and soil texture. The results indicate that inorganic carbon in the study area consists of both primary carbonate minerals and secondary pedogenic carbonates. The DOM primarily consists of two components, both identified as terrestrial humic substances. In meadow soils, bacterial activity drives the weathering of plagioclase, which releases Ca2+ necessary for the formation of pedogenic carbonates. Plagioclase also provides colonization sites for microbes and, along with microbial activity, participates in the soil carbon cycle. Within the soil community, bacteria appear to play a more critical role than fungi. In contrast, microbial contributions to the carbon cycle in swamp soils are weaker, with minerals predominantly interacting with organic carbon to form mineral-associated organic matter, thus promoting the soil carbon cycle. These findings have important implications for understanding soil carbon sinks under different micro-ecological conditions in arid and semi-arid regions. Through targeted human intervention, it is possible to enhance carbon sequestration in these areas, contributing to the mitigation of global climate change.

Biodiversity of mudflat intertidal viromes along the Chinese coasts

Viruses constitute the most diverse and abundant biological entities on Earth. However, our understanding of this tiniest life form in complex ecosystems remains limited. Here, we recover 20,102 viral OTUs from twelve intertidal zones along the Chinese coasts. Our analysis demonstrates high viral diversity and functional potential in intertidal zones, encoding important functional genes that can be potentially transferred to microbial hosts and mediate elemental biogeochemical cycles, especially carbon, phosphate and sulfur. Virus-host abundance dynamics vary among different microbial lineages. Viral community composition is closely associated with environmental conditions, including dissolved organic matter. Concordant biogeographic patterns are observed for viruses and microbes. Viral communities are generally habitat specific with low overlaps between intertidal and other habitats. Environmental factors and geographic distance dominate the compositional variation of intertidal viromes. Overall, these findings expand our understanding of intertidal viromes within an ecological framework, providing insights into the virus-host coevolutionary arms race.

Microbial communities reveal niche partitioning across the slope and bottom zones of the challenger deep

Widespread marine microbiomes exhibit compositional and functional differentiation as a result of adaptation driven by environmental characteristics. We investigated the microbial communities in both seawater and sediments on the slope (7-9 km) and the bottom (9-11 km) of the Challenger Deep of the Mariana Trench to explore community differentiation. Both metagenome-assembled genomes (MAGs) and 16S rRNA amplicon sequence variants (ASVs) showed that the microbial composition in the seawater was similar to that of sediment on the slope, while distinct from that of sediment in the bottom. This scenario suggested a potentially stronger community interaction between seawater and sediment on the slope, which was further confirmed by community assembly and population movement analyses. The metagenomic analysis also indicates a specific stronger potential of nitrate reduction and sulphate assimilation in the bottom seawater, while more versatile nitrogen and sulphur cycling pathways occur on the slope, reflecting functional differentiations among communities in conjunction with environmental features. This work implies that microbial community differentiation occurred in the different hadal niches, and was likely an outcome of microbial adaptation to the extreme hadal trench environment, especially the associated hydrological and geological conditions, which should be considered and measured in situ in future studies.

The Hunt for Chemical Dark Matter across a River-to-Ocean Continuum

Thousands of mass peaks emerge during molecular characterization of natural dissolved organic matter (DOM) using ultrahigh-resolution mass spectrometry. While mass peaks assigned to certain molecular formulas have been extensively studied, the uncharacterized mass peaks that represent a significant fraction of organic matter and convey biogenic elements and energy have been previously ignored. In this study, we introduce the term dark DOM (DDOM) for unassigned mass peaks and have explored its characteristics and environmental behaviors using a data set of 38 DOM extracts covering the Yangtze River-to-ocean continuum. We identified a total of 9141 DDOM molecules, which exhibited higher molecular weight and greater diversity than the DOM subset with assigned DOM formulas. Although DDOM contributed a smaller fraction of relative abundance, it significantly impacted the molecular weight and molecular composition of bulk DOM. A portion of DDOM with higher molecular weight was found to increase molecular abundance across the river-to-ocean continuum. These compounds could contain halogenated organic molecules and might have a high potential to contribute to the refractory organic carbon pool. With this study, we underline the contribution of dark matter to the total DOM pool and emphasize that more DDOM research is needed to understand its contribution to global biogeochemical cycles and carbon sequestration.

The microbial carbon pump and climate change

The ocean has been a regulator of climate change throughout the history of Earth. One key mechanism is the mediation of the carbon reservoir by refractory dissolved organic carbon (RDOC), which can either be stored in the water column for centuries or released back into the atmosphere as CO2 depending on the conditions. The RDOC is produced through a myriad of microbial metabolic and ecological processes known as the microbial carbon pump (MCP). Here, we review recent research advances in processes related to the MCP, including the distribution patterns and molecular composition of RDOC, links between the complexity of RDOC compounds and microbial diversity, MCP-driven carbon cycles across time and space, and responses of the MCP to a changing climate. We identify knowledge gaps and future research directions in the role of the MCP, particularly as a key component in integrated approaches combining the mechanisms of the biological and abiotic carbon pumps for ocean negative carbon emissions.

Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments

Heavy metals can impact the structure and function of coastal sediment. The dissolved organic matter (DOM) pool plays an important role in determining both the heavy metal toxicity and microbial community composition in coastal sediments. However, how heavy metals affect the interactions between microbial communities and DOM remains unclear. Here, we investigated the influence of heavy metals on the microbial community structure (including bacteria and archaea) and DOM composition in surface sediments of Beibu Gulf, China. Our results revealed firstly that chromium, zinc, cadmium, and lead were the heavy metals contributing to pollution in our studied area. Furthermore, the DOM chemical composition was distinctly different in the contaminated area from the uncontaminated area, characterized by a higher average O/C ratio and increased prevalence of carboxyl-rich alicyclic molecules (CRAM) and highly unsaturated compounds (HUC). This indicates that DOM in the contaminated area was more recalcitrant compared to the uncontaminated area. Except for differences in archaeal diversity between the two areas, there were no significant variations observed in the structure of archaea and bacteria, as well as the diversity of bacteria, across the two areas. Nevertheless, our co-occurrence network analysis revealed that the B2M28 and Euryarchaeota, dominating bacterial and archaeal groups in the contaminated area were strongly related to CRAM. The network analysis also unveiled correlations between active bacteria and elevated proportions of nitrogen-containing DOM molecules. In contrast, the archaea-DOM network exhibited strong associations with nitrogen- and sulfur-containing molecules. Collectively, these findings suggest that heavy metals indeed influence the interaction between microbial communities and DOM, potentially affecting the accumulation of recalcitrant compounds in coastal sediments.

Spatial distribution characteristics of carbazole and polyhalogenated carbazoles in water column and sediments in the open Western Pacific Ocean

Polyhalogenated carbazoles (PHCZs), an emerging persistent halogenated organic pollutant, have been detected in the environment. However, our understanding of PHCZs in the ocean remains limited. In this study, 47 seawater samples (covering 50 - 4000 m) and sediment samples (49 surface and 3 cores) were collected to investigate the occurrence and spatial distribution patterns of carbazole and its halogenated derivants (CZDs) in the Western Pacific Ocean. In seawater, the detection frequencies of CZ (97.87%) and 3-CCZ (57.45%) were relatively high. In addition, the average concentration of ΣPHCZs in the upper water (< 150 m, 0.23 ± 0.21 ng/L) was significantly lower than that in the deep ocean (1000 - 4000 m, 0.65 ± 0.56 ng/L, P < 0.05), which may indicate the vertical transport of PHCZs in the marine environment. The concentration of ΣCZDs in surface sediment ranges from 0.46 to 6.48 ng/g (mean 1.54 ng/g), among which CZ and 36-CCZ were the predominant components. Results from sediment cores demonstrate a noteworthy negative correlation between the concentration of CZDs and depth, indicating the ongoing natural degradation process occurring in sediment cores over a long period. This study offers distinctive insights into the occurrence, composition, and vertical features of CZDs in oceanic environments.

Co-influence of biochar-supported effective microorganisms and seasonal changes on dissolved organic matter and microbial activity in eutrophic lake

DOM (dissolved organic matter) play a crucial role in lakes' geochemical and carbon cycles. Eutrophication evolution would influence nutrient status of waters and investigating the DOM variation helps a better understanding of bioremediation on environmental behavior of DOM in eutrophic lakes. In our study, the contents, compositions and characteristics of systematic DOM&SOM (sediment organic matter) were greatly influenced by seasonal changes. But the effective bioremediations obviously reduced the DOM concentration and thus mitigated the eutrophication outbreak risks in water bodies due to the increased MBC (microbial biomass carbon), microbial activity and metabolism. In early summer, the overall DOM in each treatment were readily low levels and derived from both autochthonous and exogenous origins, dominated by fulvic acid-like. In midsummer, the DOM contents and characteristics in each treatment increased significantly as phytoplankton activity improved, and the majority of DOM were humic acid-like and mainly of biological origin. The greatest differences of enzymes, MBC, microbial metabolism and DOM&SOM removal among different treatments were observed in summer months. In autumn, the systematic DOM&SOM slightly reduced due to the deceased microbial activity, in which the microbial humic acids were main component and derived from endogenous sources. Additionally, the gradually decreased SOM with cultivated time in each treatment was a result of microbiological conversion of SOM into DOM. For various treatments, BE, BE.A, BE.C and BE.E increased the MBC, enzymatic and microbial activities due to the application of biochar-supported EMs. Among these, BE and BE.A, especially BE.A with oxygen supplement, achieved the most desirable effect on reducing systematic DOM&SOM levels and increasing enzymatic and microbial activities. The group of EM also reduced the levels of DOM&SOM as improved degradation of EMs for DOM. However, BC, BE.C and BE.E finally did not achieved the desirable effect on reducing DOM&SOM due to the suppression of microbial activities, respectively, from high dose of biochar, weakening of dominant species and additional introduction of EMs in low liveness.

Differences in Dissolved Organic Matter Molecular Composition along Two Plume Trajectories from the Yangtze River Estuary to the East China Sea

Analyzing the molecular composition change of dissolved organic matter (DOM) during transportation in estuaries can enhance our understanding of the fate of DOM. However, the impact of hydrologic conditions resulting from large river plumes on the DOM cycle are less explored, and previous studies were insufficient to capture the molecular fate that occur during the transportation process. In this study, we used a range of bulk and optical techniques, as well as Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), to determine the concentration and characteristics of DOM along two trajectories of downstream plumes of diluted water of the Yangtze (Changjiang) River estuary (YRE) during the high discharge season. These two plumes situated along the route of the summer Changjiang diluted water (CDW) have been identified and named CDW-North (CDW-N) and CDW-South (CDW-S), respectively. Despite having the same riverine end-member origin, the turbidity zone in YRE significantly modifies the molecular characteristics and composition of DOM. The results of FT-ICR MS indicated a spatial variation of DOM composition in the coastal zone of the two plumes. The relative intensities of the CHO, CHOS, and CHONS compounds are negatively correlated with salinity. In addition, the coastal zones of both CDW-N and CDW-S are characterized by more autochthonous DOM sources. More CHON compounds in CDW-N are probably due to the production of autochthonous DOM in offshore waters. The activity of phytoplankton increased the surface dissolved oxygen level of CDW-N in the coastal zone. However, the hypoxic zone formed at the bottom of the CDW-N due to microbial degradation of organic matter and may further benefit the preservation of CHON compounds. Our study emphasizes that the characteristics and composition of the estuarine DOM can be significantly shaped by distinct large river plumes. Furthermore, using FT-ICR MS in combination with complementary techniques can better assist in identifying the sources and transformation mechanisms of estuarine DOM in large river plume-affected systems and provide more valuable insights into the role of DOM in the estuarine biogeochemical cycle.