Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles

Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation

Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.

Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean

The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.

Polysaccharide preferred minority-dominant community assembly and exoenzyme enrichment in transparent exopolymer particles: Implication for global carbon cycle in water

The ubiquitous transparent exopolymer particles (TEPs) are an important organic carbon pool and an ideal microhabitat for bacteria in aquatic environments. They play a crucial role in the global carbon cycle. Organic matter transformation and carbon turnover in TEPs strongly depend on the assembly of their associated bacterial communities and enzyme activity. However, the mechanisms of bacterial community assembly and their potential effects on the organic carbon cycle in TEPs are still unclear. In this study, we comparatively explored the community assembly of TEP-associated bacteria and bacterioplankton from surface freshwater using metagenomics. It was found that the bacterial community assembly in TEPs followed a minority-dominant rule and was governed by homogeneous selection. Pseudomonadota and Actinomycetota, which are responsible for polysaccharide degradation, serve as taxon-specific biomarkers among the abundant and diverse bacteria in TEPs. The network of TEP-associated bacteria displayed stronger robustness than that of bacterioplankton. Bin 76 (majorly Acinetobacter) was the overwhelmingly dominant taxa in TEPs, whereas there was no clearly dominant taxa in TEP-free water. Exoenzyme analysis showed that 64 out of 71 identified polysaccharide hydrolases were markedly linked with the dominant bin 76 in TEPs, while no such linkage was observed for bacterioplankton. Generally, Acinetobacter, which is capable of utilizing polysaccharides, is preferred to be assembled in TEPs together with high polysaccharide hydrolase activity. This may significantly accelerate the turnover of organic carbon in the giant global TEP pool. These findings are important for a deep understanding of the carbon cycle in water.

Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides

BACKGROUND

Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses.

RESULTS

Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria.

CONCLUSIONS

Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.

The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone

The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.

Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally mixed coastal temperate habitat

Coastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonisation by macroalgae that mostly store carbon as glycans, contributing substantially to local and global carbon sequestration. Because they control carbon and energy fluxes, algae-degrading microorganisms are crucial for coastal ecosystem functions. Environmental surveys revealed consistent seasonal dynamics of alga-associated bacterial assemblages, yet resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we specifically investigated the seasonal dynamics of abundance and activity for a well-known alga-degrading marine flavobacterial genus in a tidally mixed coastal habitat of the Western English Channel. We show that members of the genus Zobellia are a stable, low-abundance component of healthy macroalgal microbiota and can also colonise particles in the water column. This genus undergoes recurring seasonal variations with higher abundances in winter, significantly associated to biotic and abiotic variables. Zobellia can become a dominant part of bacterial communities on decaying macroalgae, showing a strong activity and high estimated in situ growth rates. These results provide insights into the seasonal dynamics and environmental constraints driving natural populations of alga-degrading bacteria that influence coastal carbon cycling.

Isolation and characterization of a novel Tenacibaculum species and a corresponding bacteriophage from a Mediterranean fish hatchery: Description of Tenacibaculum larymnensis sp. nov. and Tenacibaculum phage Larrie

Tenacibaculum larymnensis sp. nov., a novel species of the Tenacibaculum genus was isolated from a commercial fish hatchery in Greece. The novel species is phylogenetically close to T. discolor and was biochemically and genetically characterized. The genome of T. larymnensis has 3.66 Mbps length, 31.83% GC content and the genomic analysis demonstrated that it harbors a wide enzymatic repertoire suggestive of increased degrading capacity but also several virulence factors including hemolysins, secretion systems, transporters, siderophores, pili and extracellular proteins. Using the novel strain, a virulent bacteriophage designated as Tenacibaculum phage Larrie was isolated and characterized. Larrie is a novel Siphovirus with relatively large genome, 77.5 kbps with 111 ORFs, a GC content of 33.7% and an exclusively lytic lifestyle. The new phage-host system can serve as an efficient model to study microbial interactions in the aquatic environment which contribute to the nutrient cycling.

Linking lifestyle and foraging strategies of marine bacteria: selfish behaviour of particle-attached bacteria in the northern Adriatic Sea

Microbe-mediated enzymatic hydrolysis of organic matter entails the production of hydrolysate, the recovery of which may be more or less efficient. The selfish uptake mechanism, recently discovered, allows microbes to hydrolyze polysaccharides and take up large oligomers, which are then degraded in the periplasmic space. By minimizing the hydrolysate loss, selfish behaviour may be profitable for free-living cells dwelling in a patchy substrate landscape. However, selfish uptake seems to be tailored to algal-derived polysaccharides, abundant in organic particles, suggesting that particle-attached microbes may use this strategy. We tracked selfish polysaccharides uptake in surface microbial communities of the northeastern Mediterranean Sea, linking the occurrence of this processing mode with microbial lifestyle. Additionally, we set up fluorescently labelled polysaccharides incubations supplying phytodetritus to investigate a 'pioneer' scenario for particle-attached microbes. Under both conditions, selfish behaviour was almost exclusively carried out by particle-attached microbes, suggesting that this mechanism may represent an advantage in the race for particle exploitation. Our findings shed light on the selfish potential of particle-attached microbes, suggesting multifaceted foraging strategies exerted by particle colonizers.

Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders

Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of bacteria within the flavobacterial genus Zobellia to initiate the degradation of whole algal tissues, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans Dsij^T has the capacity to use fresh brown macroalgae as a sole carbon source and extensively degrades algal tissues via the secretion of extracellular enzymes, even in the absence of physical contact with the algae. Co-cultures experiments with the non-degrading strain Tenacibaculum aestuarii SMK-4^T showed that Z. galactanivorans can act as a pioneer that initiates algal breakdown and shares public goods with other bacteria. A comparison of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include oxidative stress resistance proteins, type IX secretion system proteins and novel uncharacterized polysaccharide utilization loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the metabolic and ecological strategies of pioneer microbial degraders, key players in macroalgal biomass remineralization.

Eco-phylogenetic analyses reveal divergent evolution of vitamin B12 metabolism in the marine bacterial family 'Psychromonadaceae'

Cobalamin (vitamin B₁₂ ) is an essential micronutrient required by both prokaryotes and eukaryotes. Nevertheless, with high genetic and metabolic cost, de novo cobalamin biosynthesis is exclusive to a subset of prokaryotic taxa. Many Cyanobacterial and Archaeal taxa have been implicated in de novo cobalamin biosynthesis in epi- and mesopelagic ocean respectively. However, the contributions of Gammaproteobacteria particularly the family 'Psychromonadaceae' is largely unknown. Through phylo-pangenomic analyses using concatenated single-copy proteins and homologous gene clusters respectively, the phylogenies within 'Psychromonadaceae' recapitulate both their taxonomic delineations and environmental distributions. Moreover, uneven distribution of cobalamin de novo biosynthetic operon and cobalamin-dependent light-responsive regulon were observed, and of which the linkages to the environmental conditions where cobalamin availability and light regime can be varied respectively were discussed, suggesting the impacts of ecological divergence in shaping their disparate cobalamin-related metabolisms. Functional analysis demonstrated a varying degree of cobalamin dependency for both central metabolic processes and cobalamin-mediated light-responsive regulation, and underlying sequence characteristics of cis- and trans-regulatory elements were revealed. Our findings emphasized the potential roles of cobalamin in shaping the ecological distributions and driving the metabolic evolution in the marine bacterial family 'Psychromonadaceae', and have further implications for an improved understanding of nutritional interdependencies and community metabolism modulated by cobalamin.

How Microbial Food Web Interactions Shape the Arctic Ocean Bacterial Community Revealed by Size Fractionation Experiments

In the Arctic, seasonal changes are substantial, and as a result, the marine bacterial community composition and functions differ greatly between the dark winter and light-intensive summer. While light availability is, overall, the external driver of the seasonal changes, several internal biological interactions structure the bacterial community during shorter timescales. These include specific phytoplankton-bacteria associations, viral infections and other top-down controls. Here, we uncover these microbial interactions and their effects on the bacterial community composition during a full annual cycle by manipulating the microbial food web using size fractionation. The most profound community changes were detected during the spring, with 'mutualistic phytoplankton'-Gammaproteobacteria interactions dominating in the pre-bloom phase and 'substrate-dependent phytoplankton'-Flavobacteria interactions during blooming conditions. Bacterivores had an overall limited effect on the bacterial community composition most of the year. However, in the late summer, grazing was the main factor shaping the community composition and transferring carbon to higher trophic levels. Identifying these small-scale interactions improves our understanding of the Arctic marine microbial food web and its dynamics.

Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology

Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.

Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature

The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.