Oligotrophic Environments Research Articles

Bioaerosol emission characteristics and potential risks during composting: focus on pathogens and antimicrobial resistance

In this study, we analyzed bioaerosol emission characteristics and potential risks of antimicrobial resistance (AMR) during composting using the impaction culture method and metagenomic sequencing. The results showed that the highly saturated water vapor in the emission gas mitigated particulate matter emission during the thermophilic period. About the bioaerosols, the airborne aerobic bacterial emissions were suppressed as composting enters the mature period, and the airborne fungi are usually present as single-cell or small-cell aggregates (< 3.3 μm). In addition, the microbial community structure in bioaerosols was stable and independent of composting time. Most importantly, the PM2.5 in bioaerosols contained large amounts of antibiotic resistance genes (ARGs), potential pathogens, and multidrug resistant pathogens, which were diverse and present in high concentrations. Among them, ARGs concentrations encoding 21 antibiotics ranged from –4.50 to 0.70 ppm/m3 (Log10 ARGs). Among the 89 potential human pathogens detected, Escherichia coli, Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus were the only culturable potentially multidrug resistant pathogens carrying multiple ARGs encoding resistance at high concentrations (–0.57 to 1.15 ppm/m3 (Log10 ARGs)), and were more likely to persist and multiply in oligotrophic environments. Our findings indicate that composting technology can transfer AMR from solid compost to gas phase and increase the risk of AMR transmission.

Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments

BackgroundBuilt environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.ResultsThe diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.ConclusionsThis study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome.Bh9ATT9ssZEtNaJHv1wg7GVideo

Fungal Parasite Transmission in a Planktonic Ecosystem Under Light and Nutrient Constraints.

The two main components of the planktonic ecosystem are phytoplankton and zooplankton. Fungal parasites can infect zooplankton and spread between them. In this paper, we construct a dynamic model to describe the spread of fungal parasites among zooplankton. Basic reproduction number for fungal parasite transmission among zooplankton are rigorously derived. The dynamics of this system are analyzed including dissipativity and equilibria. We further explore the effects of ecological factors on population dynamics and the relationship between fungal parasite transmission and phytoplankton blooms. Interestingly, our theoretical and numerical results indicate that a low-light or oligotrophic aquatic environment is helpful in mitigating the transmission of fungal parasites. We also show that fungal parasites on zooplankton can increase phytoplankton biomass and induce blooms.

The ultra-high affinity transport proteins of ubiquitous marine bacteria

SAR11 bacteria are the most abundant microorganisms in the surface ocean1 and have global biogeochemical importance2–4. To thrive in their competitive oligotrophic environment, these bacteria rely heavily on solute-binding proteins that facilitate uptake of specific substrates via membrane transporters5,6. The functions and properties of these transport proteins are key factors in the assimilation of dissolved organic matter and biogeochemical cycling of nutrients in the ocean, but they have remained largely inaccessible to experimental investigation. Here we performed genome-wide experimental characterization of all solute-binding proteins in a prototypical SAR11 bacterium, revealing specific functions and general trends in their properties that contribute to the success of SAR11 bacteria in oligotrophic environments. We found that the solute-binding proteins of SAR11 bacteria have extremely high binding affinity (dissociation constant >20 pM) and high binding specificity, revealing molecular mechanisms of oligotrophic adaptation. Our functional data have uncovered new carbon sources for SAR11 bacteria and enable accurate biogeographical analysis of SAR11 substrate uptake capabilities throughout the ocean. This study provides a comprehensive view of the substrate uptake capabilities of ubiquitous marine bacteria, providing a necessary foundation for understanding their contribution to assimilation of dissolved organic matter in marine ecosystems.

Evaluating the effects of desalination antiscalants on phytoplankton and bacterial communities in oligotrophic environments

Antiscalants are used in seawater desalination facilities and are typically discharged with the brine back into the coastal environment. We investigated the impact of two commonly-used antiscalants; polyphosphonates and polycarboxylates-based, on phytoplankton and bacterial communities in the oligotrophic Gulf of Aqaba (Northern Red Sea) using mesocosms simulating different antiscalants concentrations. Our results indicate that the addition of polyphosphonates or poly-carboxylates antiscalants significantly altered phytoplankton and bacterial growth, despite being ‘theoretically’ unavailable for microbial utilization. Specifically, the addition of polyphosphonates resulted in a significant eutrophication leading to increase phytoplankton and heterotrophic bacterial biomass. Contrary, the addition polycarboxylates antiscalants triggered a moderate increase in heterotrophic bacterial biomass and a slight phytoplankton loss, summing to a zero change in bacterioplankton's organic biomass. Altogether, the enhanced autotrophic/heterotrophic biomass attributed to the discharge of polyphosphonates-based antiscalants could impair the pretreatment procedure and increase fouling propensity on the reverse-osmosis membranes. Therefore, it is recommended to minimize/avoid the use of polyphosphonates antiscalants in P-limited oligotrophic seas if the brine is discharged into oligotrophic environments.

The somatic genome of Eptatretus okinoseanus reveals the adaptation to deep-sea oligotrophic environment

BackgroundHagfishes are fascinating creatures that typically inhabit the deep sea. The deep sea is characterized by its lack of sunlight, primary productivity, and diminishing biomass with increasing ocean depth. Therefore, hagfishes living in this environment must develop effective survival strategies to adapt to the limited food supply. Deep-sea hagfishes have been observed to survive without food intake for up to one year. In this study, we have assembled a high-quality somatic genome of the deep-sea hagfish (Eptatretus okinoseanus) captured below 1,000 m. We compared the genome of E. okinoseanus with the genomes of inshore hagfish, lampreys, and other related species to investigate the genetic factors underlying the deep-sea hagfish adaptations to the environment.ResultsThe E. okinoseanus somatic genome was estimated to be 1.89 Gb and assembled into 17 pseudochromosomes. Phylogenetic analysis showed that shallow-sea and deep-sea hagfishes diverged approximately 58.8 million years ago. We found Perilipin gene family was significantly expanded in deep sea E. okinoseanus, which promotes triacylglycerol storage. Furthermore, a series of genes involved in fatty acid synthesis and metabolism, blood glucose regulation, and metabolic rate regulation were also expanded, rapid evolution or positive selection, and these changes contribute to their efficiency in energy utilization. Among these genes, the positively selected gene JNK may play an important role in energy metabolism. In addition, the olfactory receptors of the deep-sea hagfish were significantly expanded to 86, and three conserved motifs present only in hagfishes olfactory receptors were identified, which may facilitate the rapid localization of carrion.ConclusionsThis study provides valuable genomic resources for insights into the survival strategies of deep-sea hagfishes in oligotrophic environments.

Chromosome-level genome assembly of a deep-sea Venus flytrap sea anemone sheds light upon adaptations to an extremely oligotrophic environment.

The Venus flytrap sea anemone Actinoscyphia liui inhabits the nutrient-limited deep ocean in the tropical western Pacific. Compared with most other sea anemones, it has undergone a distinct modification of body shape similar to that of the botanic flytrap. However, the molecular mechanism by which such a peculiar sea anemone adapts to a deep-sea oligotrophic environment is unknown. Here, we report the chromosomal-level genome of A. liui constructed from PacBio and Hi-C data. The assembled genome is 522 Mb in size and exhibits a continuous scaffold N50 of 58.4 Mb. Different from most other sea anemones, which typically possess 14-18 chromosomes per haplotype, A. liui has only 11. The reduced number of chromosomes is associated with chromosome fusion, which likely represents an adaptive strategy to economize energy in oligotrophic deep-sea environments. Comparative analysis with other deep-sea sea anemones revealed adaptive evolution in genes related to cellular autophagy (TMBIM6, SESN1, SCOCB and RPTOR) and mitochondrial energy metabolism (MDH1B and KAD2), which may aid in A. liui coping with severe food scarcity. Meanwhile, the genome has undergone at least two rounds of expansion in gene families associated with fast synaptic transmission, facilitating rapid responses to water currents and prey. Positive selection was detected on putative phosphorylation sites of muscle contraction-related proteins, possibly further improving feeding efficiency. Overall, the present study provides insights into the molecular adaptation to deep-sea oligotrophic environments and sheds light upon potential effects of a novel morphology on the evolution of Cnidaria.

Quaternary floodings in the Zanzibar Channel (NW Indian Ocean, Tanzania) – Identifying palaeoceanographic patterns and palaeoenvironment using a multiproxy study

Multiproxy palaeoenvironmental analyses represent a promising tool for complex reconstructions of continent-sea or air-sea interactions in shallow marine environments. This is in particular illustrated by the case of strong climatic variations in the late Pleistocene to mid-Holocene. A unique combination of geochemical proxies (143Nd/144Nd, 87Sr/86Sr, δ18O and δ13C isotope analyses, n-alkane analysis and biomarker study) together with micropalaeontological data (foraminifera, calcareous nannoplankton and diatoms) allowed to precisely characterise two marine floodings (mid-Holocene and late Pleistocene) in the Zanzibar Channel (NW Indian Ocean, Tanzania). The climate of the late Pleistocene interval was arid compared to the Holocene. The fully oligotrophic environment characteristic of the late Pleistocene flooding (∼115–130 ka) was episodically interrupted by intervals of intense rainfall with episodes of increased nutrient input during the mid-Holocene (∼5–10 ka). The dominance of seaweed meadows in the Holocene and late Pleistocene contrasts with the modern environment dominated by seagrass ecosystems. Relatively non-radiogenic εNd signatures in the Zanzibar Channel during the Holocene and late Pleistocene indicate a strong influence of riverine input draining the Precambrian basement on the African mainland. The main inflow of seawater was from the south, consistent with the flow direction of the East African Coastal Current and the directions of the March to October monsoon winds. A promising tool for future applications as indicators of seagrass/seaweed meadow type ecosystems may be the presence of specific diatom taxa.

The Tet-on system for controllable gene expression in the rock-inhabiting black fungus Knufia petricola

Knufia petricola is a black fungus that colonizes sun-exposed surfaces as extreme and oligotrophic environments. As ecologically important heterotrophs and biofilm-formers on human-made surfaces, black fungi form one of the most resistant groups of biodeteriorating organisms. Due to its moderate growth rate in axenic culture and available protocols for its transformation and CRISPR/Cas9-mediated genome editing, K.petricola is used for studying the morpho-physiological adaptations shared by extremophilic and extremotolerant black fungi. In this study, the bacteria-derived tetracycline (TET)-dependent promoter (Tet-on) system was implemented to enable controllable gene expression in K. petricola. The functionality i.e., the dose-dependent inducibility of TET-regulated constructs was investigated by using GFP fluorescence, pigment synthesis (melanin and carotenoids) and restored uracil prototrophy as reporters. The newly generated cloning vectors containing the Tet-on construct, and the validated sites in the K. petricola genome for color-selectable or neutral insertion of expression constructs complete the reverse genetics toolbox. One or multiple genes can be expressed on demand from different genomic loci or from a single construct by using 2A self-cleaving peptides, e.g., for localizing proteins and protein complexes in the K.petricola cell or for using K. petricola as host for the expression of heterologous genes.

Microbiodiversity Landscape Present in the Mine-Tailings of the “Sierra de Huautla” Biosphere Reserve, Mexico

Large-scale mining activities generate significant amounts of waste that accumulates in the environment. These wastes, known as mine tailings, contain high levels of heavy metals, posing risks to human health and causing severe damage to ecosystems. In this study, we determined the heavy metal content of mine tailings in the Sierra de Huautla Biosphere Reserve (REBIOSH), Mexico, and investigated their effect on microbial composition. One of the sites historically contaminated with metals was sampled in three different locations, labeled S1, S2, and S3. A fourth site free of heavy metals (S4) was also used as a control. Our results showed high levels of As, Pb, Cd, and Ag, potentially dangerous metals that exceed thresholds set by international regulatory agencies. Metal contamination indices indicated moderate to extreme enrichment for As, Cd, and Pb, posing potential ecological risks. A metagenomic study of mine tailings showed a core specie-specific microbiome covered by Sinimarinibacterium flocculans, Jiangella anatolica, Thiobacillus denitrificans, Fontimonas thermophile, Sphingomonas koreensis. These may be associated with the processing of heavy metals. A comparative study using the ALDEx2 revealed that less represented species like Variovorax paradoxus, Usitatibacter rugosus, Usitatibacter palustris, Sphingosinicella microcystinivorans, Sphingobium yanoikuyae, and Stella humosa may serve as microbial markers in metal-contaminated environments. In addition, we detected rare or low-abundance species belonging to the phylum Armatimonadota, Candidatus Melainobacteriota, Candidatus Saccharimonadota, Chlamydiota, Deinococcota, Elusimicrobiota, Bacillota, Rhodothermota and Verrucomicrobiota, which could play an important role in ecosystems contaminated with heavy metals. Also, we found site-specific taxonomic representatives such as Nitrososphaera gargensis and Nitrospira nitrificans dominating the S3 ecosystem; Ensifer aridi (S2 and S1), N. nitrificans (S2), while Reyranella soli dominate the S1 soil. These organisms could be crucial for nitrogen access in oligotrophic environments and underscore the adaptability of microbial life to extreme conditions. This is the first comprehensive study of the microbial composition in this important ecological site of the Mexican geography and can provide future guidance for the management and biological treatment of mining wastes.

Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem

ABSTRACT Pinibarrenia chlamydospora, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on Arabidopsis, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.

Picocyanobacterial-bacterial interactions sustain cyanobacterial blooms in nutrient-limited aquatic environments

Cyanobacterial blooms (CBs) and concomitant water quality issues in oligotrophic/mesotrophic waters have been recently reported, challenging the conventional understanding that CBs are primarily caused by eutrophication. To elucidate the underlying mechanism of CBs in nutrition-deficient waters, the changes in Chlorophyll a (Chl-a), cyanobacterial-bacterial community composition, and certain microbial function in Qingcaosha Reservoir, the global largest tidal estuary storage reservoir, were analyzed systematically and comprehensively after its pilot run (2011–2019) in this study. Although the water quality was improved and stabilized, more frequent occurrences of bloom level of Chl-a (>20 μg L−1) in warm seasons were observed during recent years. The meteorological changes (CO2, sunshine duration, radiation, precipitation, evaporation, and relative humidity), water quality variations (pH, total organic carbon content, dissolved oxygen, and turbidity), accumulated sediments as an endogenous source, as well as unique estuarine conditions collectively facilitated picocyanobacterial-bacterial coexistence and community functional changes in this reservoir. A stable and tight co-occurrence pattern was established between dominant cyanobacteria (Synechococcus, Cyanobium, Planktothrix, Chroococcidiopsis, and Prochlorothrix) and certain heterotrophic bacteria (Proteobacteria, Actinobacteria, and Bacteroidetes), which contributed to the remineralization of organic matter for cyanobacteria utilization. The relative abundance of chemoorganoheterotrophs and bacteria related to nitrogen transformation (Paracoccus, Rhodoplanes, Nitrosomonas, and Zoogloea) increased, promoting the emergence of CBs in nutrient-limited conditions through enhanced nutrient recycling. In environments with limited nutrients, the interaction between photosynthetic autotrophic microorganisms and heterotrophic bacteria appears to be non-competitive. Instead, they adopt complementary roles within their ecological niche over long-term succession, mutually benefiting from this association. This long-term study confirmed that enhanced nutrient cycling, facilitated by cyanobacterial-bacterial symbiosis following long-term succession, could promote CBs in oligotrophic aquatic environments devoid of external nutrient inputs. This study advances understanding of the mechanisms that trigger and sustain CBs under nutritional constraints, contributing to developing more effective mitigation strategies, ensuring water safety, and maintaining ecological balance.

A novel paraffin-based N/P controlled-release material for biostimulation of phenol biodegradation in groundwater

To address the problem of the weak natural restoration ability of oligotrophic groundwater environments, a novel N/P controlled-release material (CRM) for biostimulation, prepared by an improved method, was developed. CRMs can encapsulate N and P (N/P) salts for sustained release in aquifers. Paraffin-based CRMs can be used to control N/P release rates by adjusting the particle size of CRMs and the mass ratio of the paraffin. The developed CRMs had a more remarkable adaptability to groundwater than other materials. Specifically, 0.4-cm CRMs released N/P stably and efficiently over a wide temperature range (7–25 ℃), and the release properties of various CRMs were not affected by pH. The release of N/P followed Fickian diffusion, and a dissolution-diffusion model was established to elucidate the mechanism of the controlled release. In contrast to bare N/P, CRMs obviously enhanced the biodegradation rate of phenol and prolonged the effectiveness of supplying N/P. The degradation rate of phenol in the CRM system increased by 20.8 %. The different supply modes of N/P, CRMs and bare N/P, resulted in differences in salinity. Metagenomic analysis showed that this difference changed the proportion of various phenol-degrading genera and thus changed the abundance of genes associated with the phenol degradation pathway.

Shallow-water redox changes and nitrogen cycles in the early Cambrian Nanhua Basin, South China

Widespread oceanic anoxia has been frequently invoked for metazoan extinctions during the Cambrian. However, this hypothesis remains to be debated. In this study, we measured total organic carbon (TOC), total bulk nitrogen (TNbulk), iron speciation, major and trace elements, and isotopic compositions of sedimentary bulk nitrogen (δ15Nbulk) for the Shiyantou Formation in the Meishucun section. Our results suggest ferruginous conditions and high productivity in the lower member (LM: 0–16.0 m), dominantly suboxic conditions and low productivity in the middle member (MM: 16.0–23.7 m), and oxic conditions and low productivity in the upper member (UM: 23.7–28.0 m). Low δ15Nbulk values (average 1.0 ‰) in the LM suggest quantitative assimilation of NH4+ and strong nitrogen fixation as a consequence of high primary productivity and widespread water-column reducing conditions in the Nanhua Basin. δ15Nbulk values close to 0 ‰ in the MM suggest intense nitrogen fixation owing to quantitative denitrification and anammox in an oligotrophic environment. Low δ15Nbulk values (average 1.2 ‰) in the UM are indicative of marine nitrogen limitations in an oligotrophic environment. These findings suggest a similar range of low δ15Nbulk values might result from different environments. In comparison with marine redox conditions and δ15Nbulk data from the other coeval sections in the Nanhua Basin, we propose that widespread anoxic conditions might cause the extinction of small shelly faunas. More importantly, the oligotrophic environment and anoxic conditions might delay the recovery of small shelly faunas in the shallow and deep waters of the Nanhua Basin, respectively.

Genome streamlining in Parcubacteria transitioning from soil to groundwater

BackgroundTo better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.ResultsBacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation – CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.ConclusionsOverall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.

Differential Mechanisms of Microbial As(III) and Sb(III) Oxidation and Their Contribution to Tailings Reclamation.

Mine tailings are extremely oligotrophic environments frequently contaminated with elevated As and Sb, making As(III) and Sb(III) oxidation potentially important energy sources for the tailing microbiome. Although they have been proposed to share similar metabolic pathways, a systemic comparison of the As(III) and Sb(III) oxidation mechanisms and energy utilization efficiencies requires further elucidation. In this study, we employed a combination of physicochemical, molecular, and bioinformatic analyses to compare the kinetic and genetic mechanisms of As(III) and Sb(III) oxidation as well as their respective energy efficiencies for fueling the key nutrient acquisition metabolisms. Thiobacillus and Rhizobium spp. were identified as functional populations for both As(III) and Sb(III) oxidation in mine tailings by DNA-stable isotope probing. However, these microorganisms mediated As(III) and Sb(III) oxidation via different metabolic pathways, resulting in preferential oxidation of Sb(III) over As(III). Notably, both As(III) and Sb(III) oxidation can facilitate nitrogen fixation and phosphate solubilization in mine tailings, with Sb(III) oxidation being more efficient in powering these processes. Thus, this study provided novel insights into the microbial As(III) and Sb(III) oxidation mechanisms and their respective nutrient acquisition efficiencies, which may be critical for the reclamation of mine tailings.

Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep-sea biosphere.

The NC10 phylum links anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophic pathway. Although numerous amplicon-based studies revealed the distribution of this phylum, comprehensive genomic insights and niche characterization in deep-sea environments were still largely unknown. In this study, we extensively surveyed the NC10 bacteria across diverse deep-sea environments, including waters, sediments, cold seeps, biofilms, rocky substrates, and subseafloor aquifers. We then reconstructed and analysed 38 metagenome-assembled genomes (MAGs), and revealed the extensive distribution of NC10 bacteria and their intense selective pressure in these harsh environments. Isotopic analyses combined with gene expression profiling confirmed that active nitrite-dependent anaerobic methane oxidation (n-DAMO) occurs within deep-sea sediments. In addition, the identification of the Wood-Ljungdahl (WL) and 3-hydroxypropionate/4-hydroxybutyrat (3HB/4HP) pathways in these MAGs suggests their capability for carbon fixation as chemoautotrophs in these deep-sea environments. Indeed, we found that for their survival in the oligotrophic deep-sea biosphere, NC10 bacteria encode two branches of the WL pathway, utilizing acetyl-CoA from the carbonyl branch for citric acid cycle-based energy production and methane from the methyl branch for n-DAMO. The observed low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS) in n-DAMO-related genes across these habitats suggest a pronounced purifying selection that is critical for the survival of NC10 bacteria in oligotrophic deep-sea environments. These findings not only advance our understanding of the evolutionary adaptations of NC10 bacteria but also underscore the intricate coupling between the carbon and nitrogen cycles within deep-sea ecosystems, driven by this bacterial phylum.

Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes.

Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows for proliferation. Genome streamlining is associated with genomic properties such as %GC content, genes encoding sigma factors, percent coding regions, gene redundancy, and functional shifts in processes like cell motility and ATP binding cassette transporters, among others. The current study aims to unveil the impact of nutrition on the genome size, %GC content, and functional properties of pelagic freshwater bacteria. We do this at finer taxonomic resolutions for many metagenomically characterized communities. Our study confirms the interplay of trophic level and genomic properties. It also highlights that different nutrient types, particularly phosphorus and nitrogen, impact these properties differently. We observed a covariation of functional traits with genome size. Larger genomes exhibit enriched pathways for motility, environmental interaction, and regulatory genes. ABC transporter genes reflect the availability of nutrients in the environment, with small genomes presumably relying more on metabolites from other organisms. We also discuss the distinct strategies different phyla adopt to adapt to oligotrophic environments. The findings contribute to our understanding of genomic adaptations within complex microbial communities.

Phosphomonoesterase and phosphodiesterase activities in the eastern Mediterranean in two contrasting seasonal situations

Abstract. Hydrolysis of dissolved organic phosphorus by marine planktonic microorganisms is a key process in the P cycle, particularly in P-depleted, oligotrophic environments. The present study assessed spatiotemporal variations in phosphomonoesterase (PME) and phosphodiesterase (PDE) activities using concentration kinetics in the eastern Mediterranean Sea in two contrasting situations: the end of winter (including a small bloom period) and autumn. The distribution and regulation of the maximum hydrolysis rate (Vm) and half-saturation constant (Km) of both ectoenzymes were assessed in relation to the vertical structure of the epipelagic layers. PME reached its maximum activities (Vm) after the addition of 1 µM MUF-P (4-methylumbelliferyl phosphate), whereas, for PDE, it was necessary to add up to 50 µM bis(4-methylumbelliferyl)phosphate (bis-MUF-P) to reach saturation state. On average, the Km of PDE was 33 ± 25 times higher than that of PME. The Vm of PME and Vm of PDE were linearly correlated. Conversely to the Km values, Vm values were on the same order of magnitude for both ectoenzymes, with their ratio (Vm PME : Vm PDE) ranging between 0.2 and 6.3. Dissolved organic phosphorus (DOP) and the phosphomonoesterase hydrolysable fraction of DOP explained most of the lack of variability in Vm PME and Vm PDE. On the contrary, Vm of both phosphohydrolase enzymes was inversely correlated to the concentration of dissolved inorganic phosphorus. The particular characteristics of concentration kinetics obtained for PDE (saturation at 50 µM, high Km, high turnover times) are discussed with respect to the possible unequal distribution of PDE and PME among the size continuum of organic material and accessibility of phosphodiesters.

Biogeochemical factors regulating photosynthetically dissolved organic carbon produced by phytoplankton in the Taiwan Strait

The distribution and mechanisms of photosynthetically dissolved organic carbon (PDOC) released by marine phytoplankton are frequently neglected and inadequately understood because most studies on carbon sequestration capacity have focused on photosynthetic particulate organic carbon. In this study, percentage extracellular release (PER) and its environmental influencing factors were investigated for 10 cruises in the Taiwan Strait during 2006–2023. The results indicated that the PER increased horizontally from the nearshore to the off-shelf and vertically from the surface to the bottom within the euphotic zone. PER tends to be low in eutrophic waters such as upwellings and estuaries and high in oligotrophic waters. The study revealed that the average contribution of PDOC to total primary productivity (TPP) in the Taiwan Strait could reach 18.2 ± 11.7%, which is similar to the previously estimated global oceanic values. PDOC production satisfied approximately 25% the carbon requirements of heterotropic bacteria (HB). A detailed analysis of the PER combined with model simulations proved that the distribution of the PER in the Taiwan Strait was caused by the joint contribution of irradiance, size-fractionated phytoplankton, and nutrient stoichiometry. Our results contradict the view that the PER is a constant factor that is unaffected by TPP. However, there was a significant negative correlation between the PER and TPP. The PDOC was always lower than the bacterial carbon demand for a broad range of bacterial growth efficiencies, suggesting a weak coupling between phytoplankton exudation and bacterial metabolism. This challenges the idea that there is a well-coupled relationship between bacteria and phytoplankton present on the continental shelf. These findings indicate significant discrepancies in PDOC mechanisms and the quantitative importance of nearshore eutrophic and off-shelf oligotrophic environments. Consequently, it is unwise to use uniform PERs without differentiation under trophic conditions when reevaluating and appraising marine carbon fixation.