Biogeochemical Significance Research Articles

Influence of phytoplankton, bacteria and viruses on nutrient supply in tropical waters

Diel investigations of water environments are one means to holistically understand the dynamics and functional roles of phytoplankton, bacteria and viruses in these ecosystems. They have the potential to substantially impact carbon (C), nitrogen (N) and phosphorus (P) biogeochemistry through their respective roles. This study characterizes the phytoplankton, bacteria and virus communities and the elemental composition of various C, N and P nutrients flow over three diel cycles in tropical urban lake. Our results show that ratios of C:N:P fluctuated strongly from the lack of dissolved organic phosphorus (DOP) and PO4. Specifically, green algae peaked during day time and exudate dissolved organic matter (DOM) that strongly modulate dissolved organic carbon (DOC):DOP ratio to diel DOP limitation. Multiple linear regression and Stella modelling emphasize the roles of viruses together with Synechococcus as important nutrient recyclers of NH4 and PO4 in nutrients-limited waters. Respective normalised surface PO4 and combined surface and bottom NH4 concentration selected both viruses and Synechococcus as important drivers. Process model of N and P biogeochemical cycles can achieve 69% and 57% similar to observed concentration of NH4 and PO4, respectively. A short latent period of 9 hr was calculated, in addition to the calibrated high infectivity of viruses to Synechococcus. Taken together, the rapid turn-over between Synechococcus and viruses has biogeochemical significance, where the rapid recycling of essential nutrients allows for shortcuts in the N and P cycle, supporting a wide range of microbes.

Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus.

Kinases that synthesize inositol phosphates (IPs) and pyrophosphates (PP-IPs) control numerous biological processes in eukaryotic cells. Herein, we extend this cellular signaling repertoire to viruses. We have biochemically and structurally characterized a minimalist inositol phosphate kinase (i.e., TvIPK) encoded by Terrestrivirus, a nucleocytoplasmic large ("giant") DNA virus (NCLDV). We show that TvIPK can synthesize inositol pyrophosphates from a range of scyllo- and myo-IPs, both in vitro and when expressed in yeast cells. We present multiple crystal structures of enzyme/substrate/nucleotide complexes with individual resolutions from 1.95 to 2.6 Å. We find a heart-shaped ligand binding pocket comprising an array of positively charged and flexible side chains, underlying the observed substrate diversity. A crucial arginine residue in a conserved "G-loop" orients the γ-phosphate of ATP to allow substrate pyrophosphorylation. We highlight additional conserved catalytic and architectural features in TvIPK, and support their importance through site-directed mutagenesis. We propose that NCLDV inositol phosphate kinases may have assisted evolution of inositol pyrophosphate signaling, and we discuss the potential biogeochemical significance of TvIPK in soil niches.

Dominance of photo over chromatic acclimation strategies by habitat-forming mesophotic red algae.

Red coralline algae are the deepest living macroalgae, capable of creating spatially complex reefs from the intertidal to 100+ m depth with global ecological and biogeochemical significance. How these algae maintain photosynthetic function under increasingly limiting light intensity and spectral availability is key to explaining their large depth distribution. Here, we investigated the photo- and chromatic acclimation and morphological change of free-living red coralline algae towards mesophotic depths in the Fernando do Noronha archipelago, Brazil. From 13 to 86 m depth, thalli tended to become smaller and less complex. We observed a dominance of the photo-acclimatory response, characterized by an increase in photosynthetic efficiency and a decrease in maximum electron transport rate. Chromatic acclimation was generally stable across the euphotic-mesophotic transition with no clear depth trend. Taxonomic comparisons suggest these photosynthetic strategies are conserved to at least the Order level. Light saturation necessitated the use of photoprotection to 65 m depth, while optimal light levels were met at 86 m. Changes to the light environment (e.g. reduced water clarity) due to human activities therefore places these mesophotic algae at risk of light limitation, necessitating the importance of maintaining good water quality for the conservation and protection of mesophotic habitats.

The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea.

Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.

Desulfovibrio mangrovi sp. nov., a sulfate-reducing bacterium isolated from mangrove sediments: a member of the proposed genus "Psychrodesulfovibrio".

"Psychrodesulfovibrio", a proposed genus within the family Desulfovibrionaceae, is a group of sulfate-reducing bacteria with biogeochemical significance but restricted child taxa availability. In this study, a strictly anaerobic bacterium, designed strain FT415T, was isolated from mangrove sediments in Futian Mangrove Nature Reserve in Shenzhen, China. The strain was Gram-stain-negative, motile, and vibrio-shaped with a single polar flagellum, which grew at the temperature range of 15-42°C (optimum 37°C), pH range of 6.0-7.5 (optimum 6.8), and in the presence of 0-36gl-1 NaCl (optimum 6gl-1 NaCl). In the presence of sulfate, electron donors including lactate, ethanol, pyruvate, malate, fumarate, succinate, cysteine, and glycerol were incompletely oxidized to acetate, and H2 and formate were used as electron donors with acetate as the carbon source by strain FT415T. Sulfate, thiosulfate, sulfide, and anthraquinone-2,6-disulfonate were reduced in the presence of lactate. Fe(III) oxide was reduced without cell growth. Fermentative growth was observed with pyruvate and cysteine. Vitamins were not required for growth. The major cellular fatty acids (> 10%) were C16:0, summed feature 10 (C18:1 c11/t9/t6 and/or unknown ECL 17.834), C16:1 cis 9, and C18:0. The major polar lipids were phosphatidylethanolamine, phospholipids, and aminolipids. The predominant menaquinone was MK-6(H2). The genomic DNA G+C content was 56.7%. Phylogenetic analysis showed that strain FT415T shared a 98.1% similarity in 16S rRNA gene sequence, an average nucleotide identity value of 84.0%, an average amino-acid identity value of 85.4%, and a digital DNA-DNA hybridization value of 25.7% with its closest relative Desulfovibrio subterraneus HN2T, which has been proposed to be transferred to the genus "Psychrodesulfovibrio". Based on phenotypic, phylogenetic, and genotypic evidence, a new species of the family Desulfovibrionaceae, Desulfovibrio mangrovi sp. nov. was proposed with the type strain FT415T (=GDMCC 1.3410T=KCTC 25525T).

Spatial and temporal dynamic response of abundant and rare aerobic denitrifying bacteria to dissolved organic matter in natural water: A case study of Lake Baiyangdian, China

Revealing the responses of abundant and rare aerobic denitrifying bacteria to dissolved organic matter (DOM) composition is essential for understanding the aquatic N cycle ecosystems. In this study, fluorescence region integration and high-throughput sequencing techniques were used to investigate the spatiotemporal characteristics and dynamic response of DOM and aerobic denitrifying bacteria. The DOM compositions were significantly different among the four seasons (P < 0.001) without spatial differences. Tryptophan-like substances (P2, 27.89–42.67%) and microbial metabolites (P4, 14.62–42.03%) were the dominant components, and DOM exhibited strong autogenous characteristics. Abundant (AT), moderate (MT), and rare taxa (RT) of aerobic denitrifying bacteria showed significant and spatiotemporal differences (P < 0.05). The responses of α-diversity and niche breadth of AT and RT to DOM differed. The DOM explanation proportion for aerobic denitrifying bacteria exhibited spatiotemporal differences based on redundancy analysis. Foliate-like substances (P3) had the highest interpretation rate of AT in spring and summer, while humic-like substances (P5) had the highest interpretation rate of RT in spring and winter. Network analysis showed that RT networks were more complex than AT networks. Pseudomonas was the main genus associated with DOM in AT on a temporal scale, and was more strongly correlated with tyrosine-like substances (P1), P2, and P5. Aeromonas was the main genus associated with DOM in AT on a spatial scale and was more strongly correlated with P1 and P5. Magnetospirillum was the main genus associated with DOM in RT on a spatiotemporal scale, which was more sensitive to P3 and P4. Special operational taxonomic units were transformed between AT and RT with seasonal changes, but not between the two regions. To summarize, our results revealed that bacteria with different abundances utilized DOM components differently, and provides new insight on the spatiotemporal response of DOM and aerobic denitrifying bacteria in aquatic ecosystems of biogeochemical significance.

Exploring the phycosphere of Emiliania huxleyi: From bloom dynamics to microbiome assembly experiments.

Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea (Eastern North Atlantic), exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions, and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota and Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. The taxonomic richness of bacteria derived from natural communities associated with axenic E. huxleyi rapidly shifted and then stabilized over time. The succession of microorganisms recruited from the environment was consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.

Soil colloidal particles in a subtropical savanna: Biogeochemical significance and influence of anthropogenic disturbances

Soil colloids (diameter < 1000 nm) are comprised mainly of clay minerals and organic matter, and play major roles in determining ion exchange capacity and in regulating key biogeochemical processes. Consequently, it is important to understand how soil colloids and their functions are influenced by land cover and anthropogenic disturbances. In grasslands, savannas, and other dryland ecosystems across the globe, woody plants are encroaching due to livestock grazing, fire suppression, elevated CO2 concentrations, and climate change. These major land cover changes could influence soil colloidal properties, with implications for soil C, N, and P cycles. We assessed how woody encroachment, livestock grazing, and fire interact to influence soil colloidal properties in a juniper-oak savanna. Surface soils (0–10 cm) from the southern Great Plains (Texas, USA) were collected from long-term treatments differing in grazing intensity (none, moderate, and heavy) and fire history. Within each treatment, soil samples were taken under grass, juniper, and oak canopies. Water dispersible soil colloids (WDC, d < 500 nm) were isolated and analyzed by asymmetric flow field-flow fractionation and their P species by liquid-state 31P-nuclear magnetic resonance spectroscopy (31P NMR). Soil beneath oak and juniper canopies had smaller WDC and elevated colloidal organic carbon (OC) and P concentrations, especially in nanocolloid (<30 nm) and fine colloid (30–160 nm) size fractions. Woody encroachment enriched Ca, Fe, Al, Si and Mg in WDC in the ungrazed control, but not in any of the other grazed or burned areas. Colloidal soil P mainly occurred as orthophosphate and orthophosphate diesters, and was present as OC-Ca-P complexes in fine and medium colloid fractions (30–500 nm), while P in the nanocolloid fraction (<30 nm) was in direct association with Ca. Moderate grazing did not affect the retention of colloidal P, while heavy grazing potentially increased the loss risk of colloidal P. Fire accelerated soil P loss from colloid fractions only in woody areas. Our findings highlight that woody encroachment strengthens the retention of OC and P by soil colloids, consequently increasing overall C and P pools in savanna soils.

Non-cyanobacterial diazotrophs: Global diversity, distribution, ecophysiology, and activity in marine waters.

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Effects of clay minerals on biogeochemical significance of viruses: A review

作为自然界丰度最高的生命体，病毒活跃于海洋、土壤、冰川等各类生态系统。通过侵染细菌、古菌及真核微生物，病毒在调控微生物群落和元素生物地球化学循环过程中扮演着关键角色。在自然环境中，病毒与无机或有机颗粒存在广泛的相互作用。黏土矿物是广泛分布于陆地和海洋环境的无机颗粒，陆地生态系统中的黏土矿物可在大气、河流和冰川的作用下搬运至海洋，并在水体中沉降形成深海沉积物。黏土矿物对病毒具有高度亲和力，影响着环境中病毒的丰度、活性和感染性，因此，黏土矿物对病毒介导的生物地球化学循环过程有着重要的影响。本文从各类生境中病毒的生态功能、病毒的生物地球化学作用模型和黏土矿物对病毒的吸附作用3个方面进行了概述，并讨论了陆地和海洋生态系统中黏土矿物的吸附作用对病毒功能和生物地球化学作用的潜在影响，提出黏土矿物是影响病毒驱动的生物地球化学循环不可忽视的因素，未来应将黏土矿物作为评估病毒生物地球化学作用的参数之一。

Microbe Profile: Geobacter metallireducens: a model for novel physiologies of biogeochemical and technological significance.

Geobacter metallireducens has served as the initial model for a substantial number of newly recognized microbial physiologies that play an important role in biogeochemical cycling of carbon, metals and nutrients. The strategies used by G. metallireducens for microbial interaction with minerals, contaminants, other microbes and electrodes have led to new technologies for bioremediation, bioenergy conversion and the sustainable production of 'green' electronics.

Bacterial community assembly in surface sediments of a eutrophic shallow lake in northern China

Anthropogenic perturbations make negative effects on wetland ecosystems, such as increasing levels of eutrophication. Under variable environmental conditions, studying the processes and mechanisms underlying their spatial distribution is critical to biogeochemical significance of microorganisms. In order to understand the changes in sediment bacterial community and their assembly with long-term eutrophication of the Baiyangdian Lake of China, we explored the microbial communities for 24 surface sediment samples using high throughput sequencing of V3-V4 region of 16S rRNA gene, meanwhile we employed Neutral community model (NCM) to characterize the community assembly processes. Then, the β-nearest taxon index (βNTI) based on a null model was used to provide a quantitative description of the assembly processes of the bacterial community. Dispersal limitation, quantified by βNTI, accounted for ∼64.6% of all assembly processes. As the increasing levels of eutrophication, deterministic processes of bacterial community assembly may be enhanced. Moreover, the significant correlation between the βNTI and change in water NO3− or sediment pH might lead to deterministic processes. There was some selection pressure acting within the Baiyangdian lake sediments. The neutral community model properly explained bacterial community assembly. The NO3−, NH4+, pH and EC were main influencing factors on the composition of the bacterial community. The overlying water NO3−, surface water NO3− and sediment pH were the three most crucial environmental factors to drive bacterial assembly. The findings revealed that Group 4 with relatively stronger deterministic processes as a more eutrophic area should be monitored as an indicator for eutrophication governance.

Dry-deposition of inorganic and organic nitrogen aerosols in Xiamen Bay: Fluxes, sources, and biogeochemical significance

Increased dry deposition of nitrogen aerosols (aerosol-N) as a result of anthropogenic emissions has caused large negative impacts on marine ecosystems. We monitored the number concentrations and sizes of inorganic nitrogen aerosols (aerosol-IN: NH4+ and NO3−) and organic nitrogen aerosols (aerosol-ON: methylamine, dimethylamine, trimethylamine, ethylamine, diethylamine, and triethylamine) by single-particle aerosol mass spectrometry (SPAMS) during the warm season (WS) and cold season (CS) of 2013 and 2015 in Xiamen Bay. The mean hourly number concentration of aerosol-IN (874/h) overwhelmed that of aerosol-ON (103/h), accounting for 83.9 ± 16.1% of aerosol-N. More than 90% of aerosol-N was concentrated in the condensation mode (0.1–0.5 μm) and droplet mode (0.5–2.0 μm). Aerosol-IN was the main contributor (80.1–94.2%) to aerosol-N deposition. New production potentially supported by the ocean's external nitrogen supply provided aerosol-N input of 11.51–11.96 g C m−2 yr−1, which contributed 17.5–18.2% of total new production in the southern East China Sea. Four potential sources of aerosol-N were identified based on the results of positive matrix factorization analysis, including secondary formation (F1), biogenic source (F2), sea spray, soil dust, biomass burning (F3), and anthropogenic sources (F4). Aerosol-N concentrations in Xiamen Bay were mainly affected by the ocean air masses during the WS and inland air masses during the CS. The percentages of aerosol-N at each backward trajectory cluster showed that the inland air masses brought more aerosol-IN emitted from biomass burning, soil dust, and secondary formation sources, whereas the ocean air masses brought more aerosol-ON emitted from a marine biogenic source into Xiamen Bay. This study provides an example of determining the number concentrations and sizes of IN and ON in aerosols by SPAMS, and helps us further understand the dry deposition and sources of IN and ON in aerosols in Xiamen Bay.

Metabolic and ecological controls on the stable carbon isotopic composition of archaeal (isoGDGT and BDGT) and bacterial (brGDGT) lipids in wetlands and lignites

The glycerol dialkyl glycerol tetraether (GDGT) lipids of archaea and bacteria have been extensively studied in both modern and ancient wetlands, but their specific biological sources and biogeochemical significance in such settings remain unclear. The stable carbon isotopic composition of GDGTs, and associated tetraether lipids such as butanetriol - DGTs (BDGTs), can help reveal aspects of the carbon metabolism of their source organism. Here we present an in-depth compound-specific analyses of archaeal (isoGDGTs and BDGT-0) and bacterial (brGDGTs) tetraether lipid δ13C values from the Florida Everglades wetland, supplemented by 16S rRNA gene profiling of the archaeal community. We interpret this alongside GDGT δ13C analyses from three additional freshwater wetland sediments, and two ancient wetland deposits (lignites) from the Miocene. Our data suggests that isoGDGT-0 δ13C values, which range from –22.5‰ to −36.5‰ across our wetland sites, could to some degree reflect the relative importance of the acetotrophic and CO2-reducing hydrogenotrophic methanogenic pathways, though definitively delineating between the two is challenging due to (a) potential incorporation of dissolved inorganic carbon (DIC) by CO2 reducers, and (b) the diluting effect of GDGTs derived from seemingly heterotrophic/fermentative Bathyarchaeia, the most abundant archaeal class in the Everglades. In the Everglades, which harbours abundant Methanomassiliicoccales, BDGT-0 is significantly more 13C-depleted than all other lipids, with a δ13C signature at certain depths (∼−40.0 to −45.0‰) that is consistent with an important source from these (likely) methylotrophic methanogens. This adds to a growing body of evidence on the underappreciated role of methylotrophic methanogenesis, largely driven by Methanomassiliicoccales, in the freshwater methane cycle. However, slightly more 13C-enriched values (∼−35.0‰) at certain depths in the same site provide evidence for additional, possibly heterotrophic sources under certain conditions, and BDGT-0 δ13C values in the Miocene lignite (≈ δ13C of TOC) are consistent with a solely heterotrophic source. Where available for measurement, δ13C values of isoGDGTs-1 to -3, averaging –32.7 ± 2.3‰, were significantly more 13C-depleted than isoGDGT-0, suggesting a different mixture of sources, likely including an autotrophic/mixotrophic component derived from archaea belonging to the Crenarchaeota, Nitrososphaeria (formerly Thaumarchaeota) and/or MBG-D/DHVEG-1. Finally, brGDGT δ13C values are generally consistent with their proposed bacterial heterotrophic origin and biosynthetic effects, averaging out at around 4‰ depleted relative to total organic carbon (TOC). Importantly, we find no significant variation between the δ13C values of different brGDGTs across our wetland types. This highlights that spatial and temporal changes in commonly applied brGDGT-based proxies likely do not co-occur with changes in the heterotrophic lifestyle of their producer(s), discounting a possible confounding factor in brGDGT palaeothermometry. Taken together, our results yield insights into wetland archaeal communities and the lipids they produce, and underline the applicability of tetraether δ13C analyses in probing aspects of microbial carbon cycling in modern and ancient wetland sediments.

Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae.

Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium). We showed that this symbiosis is very dynamic whereby symbionts interact with different host cells via extracellular vesicles within the colony. 3D electron microscopy revealed that the photosynthetic apparatus of the microalgae was more voluminous in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were stored in the symbiotic microalga in starch granules and purine crystals respectively. Nitrogen was also allocated to the algal nucleolus. In the host, low 13 C transfer was detected in the Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (c. 40 ppm) and twofold higher in the host, whereas copper concentration increased in symbionts and was detected in the host cell and extracellular vesicles. Sulfur concentration was around two times higher in symbionts (chromatin and pyrenoid) than their host. This study improves our understanding on the functioning of this oceanic photosymbiosis and paves the way for more studies to further assess its biogeochemical significance.

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera.

Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species’ survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.

Bacterial functional prediction tools detect but underestimate metabolic diversity compared to shotgun metagenomics in southwest Florida soils

Profiling the 16S-rRNA gene is a common method in microbial ecology to provide estimates of microbial diversity and abundance, but it cannot directly produce information about the functional potential of these taxa. While shotgun sequencing can provide functional information, the cost can be prohibitive for large scale comparative studies. Functional prediction tools have been developed to generate expected gene counts from 16S-rRNA amplicon data and allow for initial exploration of hypotheses prior to shotgun sequencing. PICRUSt2 and Tax4Fun2 are two such prediction tools that are becoming increasingly popular in microbial ecology studies. However, there are only a few benchmarking studies that have tested their performance, and none that focused on soils. The goal of the present study was to compare the performance of both prediction tools with each other and shotgun sequencing. We assessed prediction output from both tools used on the same samples from two sites in Southwest Florida and compared the predicted functional profiles with MG-RAST functional profiles on a shotgun-sequenced subset of samples. Shotgun and amplicon sequencing datasets showed comparable 16S rRNA gene profiles with observed differences likely stemming from PCR bias and taxa-dependent variability of 16S rRNA gene density in shotgun sequences. PICRUSt2 functional profiles represented greater relative abundances of genes in the pathway for oxidative phosphorylation, while Tax4Fun2 detected more genes from specialized metabolic pathways, such as for methane metabolism. PICRUSt2 functional profiles showed somewhat stronger correlations with shotgun-sequenced functional profiles than Tax4Fun2. However, both prediction tools significantly underestimated gene frequencies in many KEGG categories, including genes with biogeochemical significance for soil carbon- and nitrogen cycling.

Estimating variability and long-term change in sea ice primary productivity using a satellite-based light penetration index

Sea ice algae in the Southern Ocean have strong ecological and biogeochemical significance, providing a lipid-rich food-resource to keystone species such as Antarctic krill. Despite their ecological importance, estimating seasonal or interannual changes in ice algal production at the Antarctic circumpolar scale is not presently possible. We show that the product of ice concentration and irradiance penetrating into sea ice (Eice) explains 69% of the variability in ice algal production at the sector and seasonal scale estimated from two respected sea ice algae models. After allowing for a greater quantum yield of sea ice algae in summer than in other seasons we estimated a simple light-based index of potential ice algal production (Pice) and this explained 91% of the variability in modelled ice algal production. Our results suggest that between 1987 and 2017, ice algal production has generally increased with the largest increases seen off East Antarctica, the Weddell Sea, and the western Ross Sea.

Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China.

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized.

Dry-deposition of inorganic and organic nitrogen aerosols to the Arabian Sea: Sources, transport and biogeochemical significance in surface waters

Air-to-sea deposition of water-soluble total nitrogen (WSTN) can influence the primary productivity in the coastal oceans. Here, we assessed the concentrations of aerosol inorganic (WSIN: NH4+ + NO3−) and WSTN over the Arabian Sea during winter season (SS379:6–24 December 2018). The mean concentrations of NH4+ (109 ± 83 nmol m−3) overwhelm that of NO3− (32 ± 13 nmol m−3) and water-soluble organic nitrogen (WSON: WSTN-WSIN: 86 ± 81 nmol m−3), and contributing to ~50 ± 31% of WSTN mass. Significant linear relationships of WSON with water-soluble organic carbon and NH4+ with non-sea-salt (nss)-K+ is observed suggesting their common origin from biomass burning and fertilizers. Backward air mass trajectories and satellite-based fire counts further revealed their provenance in the Indo-Gangetic Plain and southern India. The concentration of NO3− moderately correlated with nssCa2+ (dust tracer), indicating heterogeneous reactive uptake on mineral aerosol surface. Despite high concentrations, the deposition fluxes of NH4+ (~9.4 ± 7.1 μmol m−2 d−1) and WSON (7.4 ± 7.0 μmol m−2 d−1) are lower than NO3− (27 ± 11 μmol m−2 d−1) because of their predominant fine nature (i.e., strong correlation with nss-SO42−). We also constrained the total annual atmospheric deposition rates of WSIN (0.94 Tg yr−1) and WSON (0.08 Tg yr−1) to the Arabian Sea during the continental outflow (November-April). The maximum dry-deposition of WSON to the Arabian Sea (0.24 Tg yr−1) is twice that of the riverine supply (0.11 Tg yr−1), highlighting the significance of aeolian sources. By using Redfield Stoichiometry, the WSTN deposition (21–73 μmol m−2 d−1) can account for <5.3% of fixed‑carbon by a primary production in the Arabian Sea.