Heterotrophic Metabolism Research Articles

Research Regarding the Autochthonous Dissolved Organic Carbon to Recalcitrant Dissolved Organic Carbon Transformation Mechanism in a Typical Surface Karst River

Autochthonic recalcitrant organic carbon is the most stable component in karst aquatic systems. Still, the processes of its generation and transformation remain unclear, which hinders the study of the mechanisms and quantitative calculations of carbon sinks in karst aquatic systems. This study collected water samples from the Li River, a typical surface karst river in Southwest China. Through in situ microbial cultivation and the chromophoric dissolved organic matter (CDOM) spectrum, changes in organic carbon components and their contents during the transformation of autochthonic dissolved organic carbon (Auto-DOC) to autochthonic dissolved recalcitrant organic carbon (Auto-RDOC) were analyzed to investigate the inert transformation processes of endogenous organic carbon. This study found that microbial carbon pumps (MCPs) promote the tyrosine-like component condensed into microbial-derived fulvic and humic components via heterotrophic bacteria metabolism, forming Auto-RDOC. During the dry season, the high level of Auto-DOC provides abundant organic substrates for heterotrophic bacteria, resulting in significantly higher Auto-RDOC production compared to the rainy season. This study provides fundamental information on the formation mechanisms of Auto-DOC in karst aquatic systems, which contributes to the assessment of carbon sinks in karst aquatic systems.

Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon.

Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea, which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.

Single Cells Polydopamine Coating of Rhodobacter Sphaeroides for Enhanced Electron Transfer

Photosynthetic bacteria are anoxygenic microorganisms with highly versatile metabolism, as they use sunlight to oxidize a broad variety of organic compounds in addition to heterotrophic and photoautotropic alternative metabolisms. Recent advances in coupling light-harvesting microorganisms with electronic components has led to a new generation of biohybrid devices based on microbial photocatalysts. These devices are limited by the poorly conductive interface between phototrophs and synthetic materials that inhibit charge transfer.Polydopamine (PDA), produced by self-assembly of dopamine, is a very versatile and bioinspired polymer with widespread applications1 mostly due its ability to adhere and cover surfaces of different chemical composition. The oxidative conditions employed for the formation of this dark insoluble polymer are mild and biocompatible and have inspired scientists to develop novel nanomaterials. Post-functionalization of PDA2 also enables fine tuning of properties. Furthermore, the ability of this monomer to self-assemble and polymerize in the bacterial growth medium was considered one of the requirements of the polymer to be used as coating material beside the tunable conductive properties and the flexible structure.Biocompatibility of dopamine was tested by in vivo addition in the growth media of the photosynthetic purple non sulphur Rhodobacter (R.) sphaeroides 3 in anoxygenic conditions. This study focuses on overcoming the bottleneck of biohybrid devices through the metabolically-driven encapsulation of photosynthetic cells with a bio-inspired conductive polymer. The treated cells show preserved light absorption of the photosynthetic pigments in the presence of dopamine concentrations ranging between 0.05 – 3.5 mM. The thickness and nanoparticle formation of the membrane-associated PDA matrix was further shown to vary with the dopamine concentrations in this range. Compared to uncoated cells, the encapsulated cells show up to a 20-fold enhancement in transient photocurrent measurements under mediatorless conditions. The biologically synthesized PDA can thus act as a matrix for electronically coupling the light-harvesting metabolisms of cells with conductive surfaces. 1Liu, Y.; Ai, K.; Lu, L. Polydopamine and its derivative materials: Synthesis and promising applications in energy, environmental, and biomedical fields. Chem. Rev. 2014, 114, 5057–5115. 2Buscemi, G., Vona, D., Ragni, R., Comparelli, R., Trotta, M., Milano, F., Farinola, G.M., Polydopamine/Ethylenediamine Nanoparticles Embedding a Photosynthetic Bacterial Reaction Center for Efficient Photocurrent Generation. Adv. Sustainable Syst. 2021, 2000303. 3 Labarile, R.; Varsalona, M.; Vona, D.; Stufano, P.; Grattieri, M.; Farinola, G. M.; Trotta, M., A novel route for anoxygenic polymerization of dopamine via purple photosynthetic bacteria metabolism. MRS Advances 2023

Integrated multi-omics analyses reveal microbial community resilience to fluctuating low oxygen in the East China sea

Climate change and eutrophication are accelerating ocean deoxygenation, leading to a global decline in oxygen levels. The East China Sea, frequently experiencing deoxygenation events, harbors diverse microbial communities. However, the response of these communities to the changing deoxygenation dynamics remains poorly understood. Here, we explored the composition and function of microbial communities inhabiting seawaters of the Changjiang Estuary and offshore areas. Our findings suggested that neutral processes significantly influenced the assembly of these communities. The overall bacterial composition demonstrated remarkable high stability across the oxygen gradient. Salinity exhibited a significantly stronger correlation with bacterial community structure than dissolved oxygen. Both metagenomics and metaproteomics revealed that all of the samples exhibited similar functional community structures. Heterotrophic metabolism dominated these sites, as evidenced by a diverse array of transporters and metabolic enzymes for organic matter uptake and utilization, which constituted a significant portion of the expressed proteins. O2 was the primary electron acceptor in bacteria even under hypoxic conditions, evidenced by expression of low- and high-affinity cytochrome oxidases. Proteins associated with anaerobic processes, such as dissimilatory sulfite reductases, were virtually undetectable. Untargeted liquid chromatography with tandem mass spectrometry analysis of seawater samples revealed a diverse range of dissolved organic matter (DOM) components in amino acids, lipids, organic acids, peptides, and carbohydrates, potentially fueling dominant taxa growth. Despite fluctuations in the abundance of specific genera, the remarkable similarity in community structure, function, and DOM suggests that this ecosystem possesses robust adaptive mechanisms that buffer against abrupt changes, even below the well-defined hypoxic threshold in marine ecosystem.

Synergistic effects of heterotrophic and phototrophic metabolism for Haematococcus lacustris grown under mixotrophic conditions

AbstractMixotrophic cultivation of Haematococcus lacustris is one of the most promising strategies to produce natural astaxanthin. During mixotrophic growth, microalgae assimilate and metabolize organic carbon in addition to photosynthetic growth, resulting in increased biomass productivity. Several studies have evaluated the effect of different organic carbon sources on mixotrophic growth in various microalgae species. However, knowledge of detailed growth kinetics as a function of substrate concentration and light intensity is lacking. In this study, the growth kinetics of H. lacustris using four different carbon sources and the effect of light under mixotrophic and photoautotrophic conditions are described. Mixotrophic cultivation showed significant differences in respect to applied substrate and achieved maximum specific growth rates of 0.91 ± 0.13, 0.19 ± 0.05, 0.36 ± 0.05, and 0.23 ± 0.05 day−1, for acetate, methanol, glucose, and glycerol, respectively. Optimal growth at mixotrophic conditions using acetate was 1.8 times higher than the sum of hetero- and photoautotrophic growth. Furthermore, the optimum light intensity was 1.3 times higher for mixotrophic than for autotrophic growth. Thus, mixotrophy increases light intensity tolerance. These results indicate a strong interconnection between carbon metabolism and photosynthetic activity and lay the foundation for more detailed mathematical models describing the mixotrophic growth of H. lacustris. Graphical Abstract

Deciphering the anammox microbial community succession with humic acid exposure to optimize large anammox granules for robust nitrogen removal

The robustness of the anaerobic ammonia oxidation (anammox) process in treating wastewater with high concentrations of humic acids (HAs), including landfill leachate and sludge anaerobic digestion liquid, has been paid great attention. This study revealed that the anammox sludge granule size of 1.0–2.0 mm could be robust under the HA exposure with high concentrations. The total nitrogen removal efficiency (NRE) was 96.2% at the HA concentration of 20–100 mg/L, while the NRE was 88.5% at the HA concentration of 500 mg/L, with reduced by 7.7%. The increased extracellular polymeric substances (EPS) content which was stimulated by the HA exposure favored the formation of large granules (1.0–2.0 mm) by enveloping medium and micro granules (0.2–1.0 mm). The abundance of anammox bacteria Candidatus Brocadia was found to be higher (14.2%) in large anammox granules sized 1.0–2.0 mm, suggesting a potentially high anammox activity. However, the abundance of denitrifiers Denitratisoma increased by 4.3% in ultra-large anammox granules sized >2.0 mm, which could be attributed to the high EPS content for heterotrophic denitrifiers metabolism as organic matter. The feedback mechanism of the anammox community for maintaining the ecological function under the HA exposure resulted in a closely related microbial community, with positive and negative correlations in the ecological network increased by 64.3%. This study revealed that the HA exposure of the anammox system resulted in the anammox granules of 1.0–2.0 mm size being the dominant granules with robust nitrogen removal, providing significant guidance for the optimization of anammox granules for an efficient treatment of HA-containing wastewater in anammox applications.

Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon.

Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.

Buried particulate organic carbon fuels heterotrophic metabolism in the hyporheic zone of a montane headwater stream

Buried particulate organic carbon fuels heterotrophic metabolism in the hyporheic zone of a montane headwater stream

Microbial Autotrophy Recorded by Carbonate Dual Clumped Isotope Disequilibrium

AbstractThe proliferation of microbial carbon fixation is a key control on the evolution of the biosphere and global carbon cycle. Most records of these metabolisms in ancient rocks come from organic matter or fossils, which are not always preserved. Here, we present a potential proxy for microbial carbon fixation (autotrophy) based on the isotopic composition of carbonate minerals. Autotrophs influence carbonate chemistry in the cellular microenvironment by decreasing CO2 concentration and increasing the carbonate saturation state. This can induce rapid precipitation of carbonate minerals that are out of isotopic equilibrium with their environment. Recent work has identified disequilibrated dual clumped isotope compositions (∆47 and ∆48) in the skeletal fossils of marine calcifying organisms. Here we test whether the same is true of non‐skeletal carbonate fabrics associated with microbial autotrophs in modern and Eocene lakes. We found that microbial carbonate formed via autotrophic metabolism recorded lower ∆47 and higher ∆48 values (−∆47/+∆48) than predicted for thermodynamic equilibrium mineral formation. Our findings are supported by models of dual clumped isotope kinetics in the DIC system, and disequilibrium in the oxygen isotope system. We hypothesize that the inverse trajectory away from the equilibrium line (+∆47/−∆48) should be recorded by carbonates formed in association with alkalinizing heterotrophs, such as sulfate reducers. If so, carbonate dual clumped isotopes could be a powerful tool to identify the proliferation and rate of heterotrophic and autotrophic metabolisms in the carbonate rock record on Earth and (perhaps) other planets.

Genomic fingerprints of the world's soil ecosystems.

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.

Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode

Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.

Growth and mortality of aerobic anoxygenic phototrophs in the North Pacific Subtropical Gyre.

Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75-0.90 d-1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d-1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.IMPORTANCEMarine bacteria represent a complex assembly of species with different physiology, metabolism, and substrate preferences. We focus on a specific functional group of marine bacteria called aerobic anoxygenic phototrophs. These photoheterotrophic organisms require organic carbon substrates for growth, but they can also supplement their metabolic needs with light energy captured by bacteriochlorophyll. These bacteria have been intensively studied in coastal regions, but rather less is known about their distribution, growth, and mortality in the oligotrophic open ocean. Therefore, we conducted a suite of measurements in the North Pacific Subtropical Gyre to determine the distribution of these organisms in the water column and their growth and mortality rates. A nutrient amendment experiment showed that aerobic anoxygenic phototrophs were limited by inorganic nitrogen. Despite this, they grew more rapidly than average heterotrophic bacteria, but their growth was balanced by intense grazing pressure.

Life on Earth can grow on extraterrestrial organic carbon

The universe is a vast store of organic abiotic carbon that could potentially drive heterotrophy on habitable planets. Meteorites are one of the transporters of this carbon to planetary surfaces. Meteoritic material was accumulating on early Earth when life emerged and proliferated. Yet it is not known if this organic carbon from space was accessible to life. In this research, an anaerobic microbial community was grown with the CM2 carbonaceous chondrite Aguas Zarcas as the sole carbon, energy and nutrient source. Using a reversed 13C-stable isotope labelling experiment in combination with optical photothermal infrared (O-PTIR) spectroscopy of single cells, this paper demonstrates the direct transfer of carbon from meteorite into microbial biomass. This implies that meteoritic organics could have been used as a carbon source on early Earth and other habitable planets, and supports the potential for a heterotrophic metabolism in early living systems.

Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin

Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,1 via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,2,3,4 little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes5,6) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,7 which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.

Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats.

Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.

Leaves stimulate aquatic phosphorus uptake by dark‐grown but not by light‐grown microbial communities in sediments: A laboratory study

Abstract It is a widely discussed topic in restoration ecology to use organic carbon (OC) management to increase nutrient uptake in chronically loaded agricultural streams. However, although nitrate uptake has been shown to correlated closely with the availability of dissolved OC, this relationship is less clear for phosphate. Likewise, the role of particulate OC (POC) on stimulating nutrient uptake has to be clarified. We aimed at investigating the effects of leaf additions on the net uptake of soluble reactive phosphorus and nitrate‐nitrogen from the water column by benthic biofilms in combined laboratory flume and batch experiments. Fine sediments were colonised under nutrient‐enriched conditions in the dark (dark‐grown heterotrophic biofilms) and under a 12/12‐hr dark/light cycle (light‐grown photoautotrophic biofilms) in flumes. In each light treatment, half of the biofilms were grown under strong OC‐limitation, the other half under near‐optimal C:N:P ratios. For the uptake experiments, the colonised sediments were incubated in nutrient‐enriched water to which (1) fresh alder leaves, (2) pre‐leached leaves, or (3) no leaves were added. Net nutrient uptake (or release) rates were determined via the change in nutrient concentrations in the water column over time. Net phosphorus uptake by dark‐grown biofilms was significantly increased by the addition of leaves. Despite their high initial nutrient leaching, fresh leaves showed stronger stimulating effects on the net P uptake than leached leaves over the entire experiment. Furthermore, biofilms grown under near‐optimum C:N:P ratios responded stronger to the POC supply than biofilms grown under C‐limited conditions. In contrast to dark‐grown biofilms, leaf additions had no significant effects on the net P uptake by light‐grown biofilms. We also found no effects of leaf additions on net nitrate uptake. Our study shows that an increased POC supply in nutrient‐impacted streams may boost heterotrophic phosphate uptake. However, the stimulating effect of the POC addition depends on a variety of POC‐dependent (e.g. respiration, heterotrophic assimilation, denitrification) and independent (e.g. adsorption, photoautotrophic assimilation) processes, making nutrient control via POC management challenging. We suggest application of management approaches that focus on restoration of riparian areas and wetlands to increase the amount of natural, complex POC with a moderate degradability, thus keeping the heterotrophic metabolism low but potentially stimulating in‐stream N and P retention.

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

The stable carbon and hydrogen isotopic composition of microbial fatty acids traces microbial metabolism in soils and peats

The compound-specific stable carbon (δ13C) and hydrogen (δ2H) isotopic compositions of microbial fatty acids have been widely used to trace microbial metabolism across a range of mesophilic environments. However, few studies have combined the δ13C and δ2H values of microbial fatty acids. So far none have determined the δ2H of microbial phospholipid fatty acids (PLFAs) in soils or peats, even though these stable isotope combinations could provide new insights into soil microbial metabolism. Here, we measured the δ13C and δ2H values of microbial PLFAs in top soils from peatlands, meadows, and woodlands in the Dajiuhu basin, central China. We observed a significant (p < 0.05) positive correlation between the δ13C and δ2H of microbial PLFAs across the three habitats studied here, indicating that central metabolic pathways affect both carbon and hydrogen isotopic compositions of microbial PLFAs. Moreover, our stable isotope data consistently indicate a relatively conservative metabolic state, which is dominated by expected heterotrophic metabolism. The exception to these observations is PLFAs associated with methanotrophs, as these appear to have decoupled carbon and hydrogen isotopes, providing an additional tool for tracing methanotrophic signals. Our results suggest that the carbon and hydrogen dual isotopic composition of microbial PLFAs can not only provide cross-validation for microbial metabolism in natural environments, but as a combined tool can also provide new insights into the perturbation of soil microbial community metabolism.

Bioremediation of rapid sand filters for removal of organic micropollutants during drinking water production

Rapid sand filtration (RSF) is used during drinking water production for removal of particles, possible harmful microorganisms, organic material and inorganic compounds such as iron, manganese, ammonium and methane. However, RSF can also be used for removal of certain organic micropollutants (OMPs). In this study, it was investigated if OMP removal in columns packed with sand from full scale RSFs could be stimulated by bioaugmentation (i.e. inoculating RSFs with sand from another RSF) and/or biostimulation (i.e. addition of nutrients, vitamins and trace-elements that stimulate microbial growth). The results showed that removal of PFOA, carbamazepine, 1-H benzotriazole, amidotrizoate and iopamidol in the columns was low (< 20 %). Propranolol and diclofenac removal was higher (50–60 %) and propranolol removal likely occurred via sorption processes, whereas for diclofenac it was unclear if removal was a combination of physical-chemical and biological processes. Moreover, bioaugmentation and biostimulation resulted in 99 % removal of gabapentin and metoprolol after 38 days and 99 % removal of acesulfame after 52 days of incubation. The bioaugmented column without biostimulation showed 99 % removal for gabapentin and metoprolol after 52 days, and for acesulfame after 80 days. In contrast, the non-bioaugmented column did not remove gabapentin, removed < 40 % metoprolol and showed 99 % removal of acesulfame only after 80 days of incubation. Removal of these OMPs was negatively correlated with ammonium oxidation and the absolute abundance of ammonia-oxidizing bacteria. 16S rRNA gene sequencing showed that OMP removal of acesulfame, gabapentin and metoprolol was positively correlated to the relative abundance of specific bacterial genera that harbor species with a heterotrophic and aerobic or denitrifying metabolism. These results show that bioaugmentation of RSF can be successful for OMP removal, where biostimulation can accelerate this removal.

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

BackgroundHeterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.MethodsSeawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.ResultsAmendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).ConclusionsThe gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean.13R5usaxM1iwstSWbHDM6jVideo