Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group

Mixotrophic growth of a ubiquitous marine diatom

Diatoms are major players in the global carbon cycle, and their metabolism is affected by ocean conditions. Understanding the impact of changing inorganic nutrients in the oceans on diatoms is crucial, given the changes in global carbon dioxide levels. Here, we present a genome-scale metabolic model (iMK1961) for Cylindrotheca closterium, an in silico resource to understand uncharacterized metabolic functions in this ubiquitous diatom. iMK1961 represents the largest diatom metabolic model to date, comprising 1961 open reading frames and 6718 reactions. With iMK1961, we identified the metabolic response signature to cope with drastic changes in growth conditions. Comparing model predictions with Tara Oceans transcriptomics data unraveled C. closterium's metabolism in situ. Unexpectedly, the diatom only grows photoautotrophically in 21% of the sunlit ocean samples, while the majority of the samples indicate a mixotrophic (71%) or, in some cases, even a heterotrophic (8%) lifestyle in the light. Our findings highlight C. closterium's metabolic flexibility and its potential role in global carbon cycling.

Quantification of microbial community assembly processes during degradation on diverse plastispheres based on physicochemical characters and phylogenetic bin-based null model analysis

To understand the differences in degradation processes depending on the chemical properties of polymers, it is necessary to both quantify the microbiome composition and evaluate the process of microbial turnover (i.e., community assembly processes) in a variety of polymer materials. In this study, using a phylogenetic bin-based null model analysis (i.e., iCAMP), we evaluated community assembly processes from original estuary water to 37 types of polymers, which provide overwhelmingly diverse niches for microbes, in 14-day incubation experiments. First, we evaluated the polymer properties related to degradation rates. Polymers with higher adipic acid (AdA) monomer exhibited higher motility, hydrophilicity, and degradation rates, whereas those with higher aromatic monomer exhibited the opposite trends. Second, microbiome composition analysis was performed, and the microbiomes were significantly changed by the AdA or aromatic content. This was consistent with the polymer properties, suggesting that polymer motility and hydrophilicity attributable to the first-order structure modify the accessibility of the enzyme to the reaction site and hence the degradation rate, resulting in differences in microbiome community composition. Finally, we determined community assembly processes from estuary water to plastics using a phylogenetic bin-based null model analysis. The importance of heterogeneous selection was higher in mobile, hydrophilic, and fast-degrading polymers, while that of homogeneous selection was lower. This suggests that the environmental difference between before and after incubation becomes significant under rapid degradation, which select microbes adapted to biofilm environments. In addition, the more stochastic turnover prevailed, the more variation in the communities (i.e., β-diversity) increased. This suggests that turnover processes not dictated by the environment lead to instability in community compositions.

Temporal variations of bacterial and eukaryotic community in coastal waters-implications for aquaculture

Despite increased attention to the aquaculture environment, there is still a lack of understanding regarding the significance of water quality. To address this knowledge gap, this study utilized high-throughput sequencing of 16S rRNA and 18S rRNA to examine microbial communities (bacteria and eukaryotes) in coastal water over different months through long-term observations. The goal was to explore interaction patterns in the microbial community and identify potential pathogenic bacteria and red tide organisms. The results revealed significant differences in composition, diversity, and richness of bacterial and eukaryotic operational taxonomic units (OTUs) across various months. Principal coordinate analysis (PCoA) demonstrated distinct temporal variations in bacterial and eukaryotic communities, with significant differences (P = 0.001) among four groups: F (January-April), M (May), S (June-September), and T (October-December). Moreover, a strong association was observed between microbial communities and months, with most OTUs showing a distinct temporal preference. The Kruskal-Wallis test (P < 0.05) indicated significant differences in dominant bacterial and eukaryotic taxa among months, with each group exhibiting unique dominant taxa, including potential pathogenic bacteria and red tide organisms. These findings emphasize the importance of monitoring changes in potentially harmful microorganisms in aquaculture. Network analysis highlighted positive correlations between bacteria and eukaryotes, with bacteria playing a key role in network interactions. The key bacterial genera associated with other microorganisms varied significantly (P < 0.05) across different groups. In summary, this study deepens the understanding of aquaculture water quality and offers valuable insights for maintaining healthy aquaculture practices. KEY POINTS: • Bacterial and eukaryotic communities displayed distinct temporal variations. • Different months exhibited unique potential pathogenic bacteria and red tide organisms. • Bacteria are key taxonomic taxa involved in microbial network interactions.

Annual recurrence of prokaryotic climax communities in shallow waters of the North Mediterranean

In temperate coastal environments, wide fluctuations of biotic and abiotic factors drive microbiome dynamics. To link recurrent ecological patterns with planktonic microbial communities, we analysed a monthly-sampled 3-year time series of 16S rRNA amplicon sequencing data, alongside environmental variables, collected at two stations in the northern Adriatic Sea. Time series multivariate analyses allowed us to identify three stable, mature communities (climaxes), whose recurrence was mainly driven by changes in photoperiod and temperature. Mixotrophs (e.g., Ca. Nitrosopumilus, SUP05 clade, and Marine Group II) thrived under oligotrophic, low-light conditions, whereas copiotrophs (e.g., NS4 and NS5 clades) bloomed at higher temperatures and substrate availability. The early spring climax was characterised by a more diverse set of amplicon sequence variants, including copiotrophs associated with phytoplankton-derived organic matter degradation, and photo-auto/heterotrophic organisms (e.g., Synechococcus sp., Roseobacter clade), whose rhythmicity was linked to photoperiod lengthening. Through the identification of recurrent climax assemblages, we begin to delineate a typology of ecosystem based on microbiome composition and functionality, allowing for the intercomparison of microbial assemblages among different biomes, a still underachieved goal in the omics era.

Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic

Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and potential carbohydrate utilisation by microbes in Atlantic waters of the Arctic. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, while the more labile β-1,3-glucan exhibited a patchy distribution. Through 'omics analysis, we identify variations in the abundance and transcription of carbohydrate degradation-related genes across samples at the community and population level. The populations contributing the most to transcription were taxonomically related to those known as primary responders and key carbohydrate degraders in temperate ecosystems, such as NS4 Marine Group and Formosa. The unique transcription profiles for these populations suggest distinct substrate utilisation potentials, with predicted glycan targets corresponding to those structurally identified in POM from the same sampling sites. By combining cutting-edge technologies and protocols, we provide insights into the carbohydrate component of the carbon cycle in the Arctic during late summer and present a high-quality dataset that will be of great value for future comparative analyses.

Microbial biogeography of the eastern Yucatán carbonate aquifer

IMPORTANCE

The extensive Yucatán carbonate aquifer, located primarily in southeastern Mexico, is pockmarked by numerous sinkholes (cenotes) that lead to a complex web of underwater caves. The aquifer hosts a diverse yet understudied microbiome throughout its highly stratified water column, which is marked by a meteoric lens floating on intruding seawater owing to the coastal proximity and high permeability of the Yucatán carbonate platform. Here, we present a biogeographic survey of bacterial and archaeal communities from the eastern Yucatán aquifer. We apply a novel network analysis software that models ecological niche space from microbial taxonomic abundance data. Our analysis reveals that the aquifer community is composed of several distinct niches that follow broader regional and hydrological patterns. This work lays the groundwork for future investigations to characterize the biogeochemical potential of the entire aquifer with other systems biology approaches.

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.

High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean

Species within the genus Alcanivorax are well known hydrocarbon-degraders that propagate quickly in oil spills and natural oil seepage. They are also inhabitants of the deep-sea and have been found in several hydrothermal plumes. However, an in-depth analysis of deep-sea Alcanivorax is currently lacking. In this study, we used multiple culture-independent techniques to analyze the microbial community composition of hydrothermal plumes in the Northern Tonga arc and Northeastern Lau Basin focusing on the autecology of Alcanivorax. The hydrothermal vents feeding the plumes are hosted in an arc volcano (Niua), a rear-arc caldera (Niuatahi) and the Northeast Lau Spreading Centre (Maka). Fluorescence in situ hybridization revealed that Alcanivorax dominated the community at two sites (1210-1565 mbsl), reaching up to 48% relative abundance (3.5 × 104 cells/ml). Through 16S rRNA gene and metagenome analyses, we identified that this pattern was driven by two Alcanivorax species in the plumes of Niuatahi and Maka. Despite no indication for hydrocarbon presence in the plumes of these areas, a high expression of genes involved in hydrocarbon-degradation was observed. We hypothesize that the high abundance and gene expression of Alcanivorax is likely due to yet undiscovered hydrocarbon seepage from the seafloor, potentially resulting from recent volcanic activity in the area. Chain-length and complexity of hydrocarbons, and water depth could be driving niche partitioning in Alcanivorax.

Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov., two novel species isolated from Sargassum, show genomic and physiological adaptations for a Sargassum-associated lifestyle

The genus Tamlana from the Bacteroidota currently includes six validated species. Two strains designated PT2-4T and 62-3T were isolated from Sargassum abundant at the Pingtan island coast in the Fujian Province of China. 16S rRNA gene sequence analysis showed that the closest described relative of strains PT2-4T and 62-3T is Tamlana sedimentorum JCM 19808T with 98.40 and 97.98% sequence similarity, respectively. The 16S rRNA gene sequence similarity between strain PT2-4T and strain 62-3T was 98.68 %. Furthermore, the highest average nucleotide identity values were 87.34 and 88.97 % for strains PT2-4T and 62-3T, respectively. The highest DNA-DNA hybridization (DDH) value of strain PT2-4T was 35.2 % with strain 62-3T, while the DDH value of strain 62-3T was 37.7 % with T. sedimentorum JCM 19808T. Growth of strains PT2-4T and 62-3T occurs at 15-40 °C (optimum, 30 °C) with 0-4 % (w/v) NaCl (optimum 0-1 %). Strains PT2-4T and 62-3T can grow from pH 5.0 to 10.0 (optimum, pH 7.0). The major fatty acids of strains PT2-4T and 62-3T are iso-C15 : 0 and iso G-C15 : 1. MK-6 is the sole respiratory quinone. Genomic and physiological analyses of strains PT2-4T and 62-3T showed corresponding adaptive features. Significant adaptation to the growth environment of macroalgae includes the degradation of brown algae-derived diverse polysaccharides (alginate, laminarin and fucoidan). Notably, strain PT2-4T can utilize laminarin, fucoidan and alginate via specific carbohydrate-active enzymes encoded in polysaccharide utilization loci, rarely described for the genus Tamlana to date. Based on their distinct physiological characteristics and the traits of utilizing polysaccharides from Sargassum, strains PT2-4T and 62-3T are suggested to be classified into two novel species, Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov. (type strain PT2-4T=MCCC 1K04427T=KCTC 92183T and type strain 62-3T=MCCC 1K04421T=KCTC 92182T).

Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia

Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.

SulfAtlas, the sulfatase database: state of the art and new developments

SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1-S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single characterized specificity (or few specificities in some cases) or to unknown substrates. Sequences are linked to their biochemical and structural information according to an expert scrutiny of the available literature. Database browsing was initially made possible both through a keyword search engine and a specific sequence similarity (BLAST) server. In this article, we will briefly summarize the experimental progresses in the sulfatase field in the last 6 years. To improve and speed up the (sub)family assignment of sulfatases in (meta)genomic data, we have developed a new, freely-accessible search engine using Hidden Markov model (HMM) for each (sub)family. This new tool (SulfAtlas HMM) is also a key part of the internal pipeline used to regularly update the database. SulfAtlas resource has indeed significantly grown since its creation in 2016, from 4550 sequences to 162 430 sequences in August 2022.