Dandan Izabel-Shen

High-throughput sequencing has transformed biodiversity assessment and ecological monitoring, yet its quantitative reliability remains unclear. Here, we assembled two experiments of nematode mock communities: one based on extracted DNA and one on individual specimens. Although DNA extraction was required in both experiments to assess the quantitative performance of the sequencing approaches, we essentially evaluated whether this performance was influenced by differences in the start material used to constructed the mock communities. Each community was analyzed using 18S and 28S metabarcoding and shotgun sequencing to evaluate their ability to resolve quantitative information. Across datasets, the number of observed taxa increased with sequencing depth despite controlled input, indicating that higher read numbers primarily revealed intragenomic variation in nematodes than true diversity. Community composition was more accurately recovered by 18S metabarcoding and shotgun sequencing than by 28S. Both sequencing approaches reflected DNA input reasonably well; however, shotgun sequencing provided more consistent abundance estimates relative to individual counts, particularly for nematodes with relatively large-bodied size. In contrast, all methods showed limited ability to accurately quantify taxa with low DNA input or small body size. Comparisons between mock community types showed strong correspondence between read abundance and DNA input, but weaker relationships with individual counts. Overall, both metabarcoding and shotgun sequencing effectively detected community-level patterns and within-taxon abundance, but shotgun sequencing was more reliable for cross-taxon quantitative comparisons. Our findings demonstrate how input material, primer choice, and sequencing approach influence the accuracy of nematode abundance estimates, and provide guidance for improving quantitative applications in nematode-based bioindication and, more broadly environmental DNA biomonitoring.

While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.

Microbial genome size can be used as a predictor to explain the ecology and metabolism of Bacteria and Archaea across major biomes. Despite their ecological significance, the contribution of microbial genome size to differences in metabolic potential of benthic and pelagic prokaryotes are poorly studied. Here, we investigated how taxonomy and microbial genome size varies between benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. We also explored the relationships between that variation, the environmental heterogeneity, and microbial functions in these habitats. By analyzing Baltic metagenomes and MAGs, we observe that pelagic brackish Bacteria and Archaea present smaller genome sizes on average than pelagic marine and freshwater prokaryotes. Moreover, we found that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). These differences in genome size persisted in Bacteria from the phyla level to the order level. For pelagic prokaryotes, the smallest genomes coded for a higher number of module steps per Mbp than bigger genomes for most of the functions, such as amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or presence of different hydrogenases. IMPORTANCE In Bacteria and Archaea, genome size is the result of strong selection pressures shaping the ecology and metabolism of microbial lineages. Thanks to the development of metagenomic analysis of environmental samples in the last three decades, we can now survey the size of their genomes, quantify their functional capabilities, and infer the role they play in the environment. Here, by using four publicly available datasets together with one new unpublished dataset, we provide new insights on how genome size, metabolism and taxonomy are linked and how they differ between sediments and water column in the Baltic Sea. Moreover, we investigate differences in genome size of pelagic microorganisms across ecosystems, from the brackish Baltic Sea to marine and freshwater Bacteria and Archaea. Our results provide a comprehensive and contrasting view between the taxonomic and genetic diversity of sediments and water column and its implications on nutrient cycling in the Baltic Sea.

Background: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. Results: The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. Conclusions: This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats.

The increasing-volume release of micropollutants into natural surface waters has raised great concern due to their environmental accumulation. Persisting micropollutants can impact multiple generations of organisms, but their microbially-mediated degradation and their influence on community assembly remain understudied. Here, freshwater microbes were treated with several common micropollutants, alone or in combination, and then transferred every 5 days to fresh medium containing the same micropollutants to mimic the repeated exposure of microbes. Metabarcoding of 16S rRNA gene makers was chosen to study the succession of bacterial assemblages following micropollutant exposure. The removal rates of micropollutants were then measured to assess degradation capacity of the associated communities. The degradation of micropollutants did not accelerate over time but altered the microbial community composition. Community assembly was dominated by stochastic processes during early exposure, via random community changes and emergence of seedbanks, and deterministic processes later in the exposure, via advanced community succession. Early exposure stages were characterized by the presence of sensitive microorganisms such as Actinobacteria and Planctomycetes, which were then replaced by more tolerant bacteria such as Bacteroidetes and Gammaproteobacteria. Our findings have important implication for ecological feedback between microbe-micropollutants under anthropogenic climate change scenarios.

With the increase of recreational boating activity and development of boating infrastructure in shallow, wave-protected areas, there is growing concern for their impact on coastal ecosystems. In order to properly assess the effects and consider the potential for recovery, it is important to investigate microbial and meiofaunal communities that underpin the functioning of these ecosystems.

Every seed germinating in soils, wastewater treatment, and stream confluence exemplify microbial community coalescence—the blending of previously isolated communities. Here, we present theoretical and experimental knowledge on how separated microbial communities mix, with particular focus on managed ecosystems.

The increasing-volume release of micropollutants into natural surface waters has raised great concern due to their environmental accumulation. Persisting micropollutants can impact multiple generations of organisms, but their microbially-mediated degradation and their influence on community assembly remain understudied. Here, freshwater microbes were treated with several common micropollutants, alone or in combination, and then transferred every 5 days to fresh medium containing the same micropollutants to mimic the repeated exposure of microbes. Metabarcoding of 16S rRNA gene makers was chosen to study the succession of bacterial assemblages following micropollutant exposure. The removal rates of micropollutants were then measured to assess degradation capacity of the associated communities. The degradation of micropollutants did not accelerate over time but altered the microbial community composition. Community assembly was dominated by stochastic processes during early exposure, via random community changes and emergence of seedbanks, and deterministic processes later in the exposure, via advanced community succession. Early exposure stages were characterized by the presence of sensitive microorganisms such as Actinobacteria and Planctomycetes, which were then replaced by more tolerant bacteria such as Bacteroidetes and Gammaproteobacteria. Our findings have important implication for ecological feedback between microbe-micropollutants under anthropogenic climate change scenarios.

Abundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at and above the genus level. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification.

Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic‐pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water‐sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton‐derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water‐sediment interface showed that bacterial α‐diversity was not affected by POM addition, while bacterial β‐diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom‐ or cyanobacteria‐favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton‐originated POM can impact bacterial dynamics at the water‐sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic‐pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.