Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

Diverse sources of fecal contamination in macroalgae wrack-affected environment adjacent to river outflow along the Baltic Sea coast

We investigated the dynamics of feces-associated microorganisms in areas with wrack accumulation in the southeastern part of the Baltic Sea. Our study covered single-day (2021 ) and multi-day (2022) observations during the recreational season. We collected water, sand, and wrack samples and assessed the abundance of fecal indicator bacteria (FIB), as well metagenomic analysis was conducted to monitor changes in microbial composition. Based on metagenomic data we identified taxa associated with feces, sewage, and ruminant sources. Human-related fecal pollution based on genetic markers correlated with the presence of Lachnospiraceae, Prevotellaceae and Rickenellacea abundance. Higher abundance and diversity of feces-associated and ruminant-associated taxa and the presence of enteric pathogens were observed when wrack accumulated near the river outflow in 2021, suggesting a potential link with fecal pollution from the river. As a preventive measure, it is recommended to remove the wrack to reduce the risk of exposure to potential enteric pathogens if it is accumulated next to the river outflow.

Impact of beach wrack on microorganisms associated with faecal pollution at the Baltic Sea Sandy beaches

We investigated whether higher quantities of faecal indicator bacteria (FIB) are in the areas with red algae-dominated wrack compared to areas without it and if the birds are the primary source of faecal pollution on sandy beaches of the Baltic Sea. Water, sand and wrack samples were collected during the recreational season, and abundances of FIB, HF183 (human faecal pollution) and GFD (bird faecal pollution) markers, as well as the presence of Salmonella and Campylobacter, were assessed. Significantly higher levels of Enterococcus spp. were found in the wrack accumulation areas in water and sand than in the areas without wrack when there was a faecal pollution event, which could be explained by entrapment and changed physico-chemical water conditions. Both faecal pollution markers were identified, however, with no apparent pattern. Campylobacter bacteria were identified in the wrack-affected water, sand, and beach wrack. While this research provides valuable insights into beach wrack serving as a reservoir for FIB, further investigations, including multi-day samplings, are necessary to gain a deeper understanding of the long-term dynamics of microbiota within red algae-dominated wrack.

Macrophytes and their wrack as a habitat for faecal indicator bacteria and Vibrio in coastal marine environments

Waterborne pathogenic bacteria, including faecal indicator bacteria and potentially pathogenic Vibrio, are a global concern for diseases transmitted through water. A systematic review was conducted to analyse publications that investigated these bacteria in relation to macrophytes (seagrasses and macroalgae) in coastal marine environments. The highest quantities of FIB were found on brown algae and seagrasses, and the highest quantities of Vibrio bacteria were on red algae. The most extensively studied macrophyte group was brown algae, green algae were the least researched. Macrophyte wrack was found to favor the presence of FIB, but there is a lack of information about Vibrio quantities in this environment. To understand the role of Vibrio bacteria that are pathogenic to humans, molecular methods complementary to cultivation methods should be used. Further research is needed to understand the underlying mechanisms of FIB and potentially pathogenic Vibrio with macrophytes and their microbiome in the coastal marine environment.

Network Analysis Indicates Microbial Assemblage Differences in Life Stages of Cladophora

Cladophora represents a microscopic forest that provides many ecological niches and fosters a diverse microbiota. However, the microbial community on Cladophora in brackish lakes is still poorly understood. In this study, the epiphytic bacterial communities of Cladophora in Qinghai Lake were investigated at three life stages (attached, floating, and decomposing). We found that in the attached stage, Cladophora was enriched with chemoheterotrophic and aerobic microorganisms, including Yoonia-Loktanella and Granulosicoccus. The proportion of phototrophic bacteria was higher in the floating stage, especially Cyanobacteria. The decomposing stage fostered an abundance of bacteria that showed vertical heterogeneity from the surface to the bottom. The surface layer of Cladophora contained mainly stress-tolerant chemoheterotrophic and photoheterotrophic bacteria, including Porphyrobacter and Nonlabens. The microbial community in the middle layer was similar to that of floating-stage Cladophora. Purple oxidizing bacteria were enriched in the bottom layer, with Candidatus Chloroploca, Allochromatium, and Thiocapsa as the dominant genera. The Shannon and Chao1 indices of epibiotic bacterial communities increased monotonically from the attached stage to the decomposing stage. Microbial community composition and functional predictions indicate that a large number of sulfur cycle-associated bacteria play an important role in the development of Cladophora. These results suggest that the microbial assemblage on Cladophora in a brackish lake is complex and contributes to the cycling of materials. IMPORTANCE Cladophora represents a microscopic forest that provides many ecological niches fostering a diverse microbiota, with a complex and intimate relationship between Cladophora and bacteria. Many studies have focused on the microbiology of freshwater Cladophora, but the composition and succession of microorganisms in different life stages of Cladophora, especially in brackish water, have not been explored. In this study, we investigated the microbial assemblages in the life stages of Cladophora in the brackish Qinghai Lake. We show that heterotrophic and photosynthetic autotrophic bacteria are enriched in attached and floating Cladophora, respectively, whereas the epiphytic bacterial community shows vertical heterogeneity in decomposing mats.

Opportunistic Macroalgae as a Component in Assessment of Eutrophication

For the last few decades, coastal eutrophication with the associated mass development of opportunistic macroalgae has increased on a global scale. Since the end of the 2000’s, the number of studies of macroalgal blooms also increased many times. Mass occurrences of such species as Cladophora spp., Ulva spp., and Spirogyra spp. caused a necessity to improve existing methods of ecological assessment and develop new ones. There are many indices based on macroalgae and developed for marine and estuarine ecosystems. However, for correct evaluation, they demand a presence of a number of species, including perennial species from the order Fucales. This requirement cannot be satisfied in fresh or brackish waters, including some estuaries, because often, the freshwater communities are dominated by only one or two opportunistic species. The present paper defines the most relevant topics in studies of macroalgal blooms and reviews indices and metrics which can be recommended for the ecological assessment in diverse habitats influenced or dominated by opportunistic macroalgae species. For ecological assessment of opportunistic communities, according to their seasonal peculiarities, the author recommends, besides biomass, involving evaluation of algal mats (thickness, coverage) and signs of hypoxia.

Modelling the transport of sloughed cladophora in the nearshore zone of Lake Michigan

The invasion of dreissenid mussels has profoundly altered benthic physical environments and whole-lake nutrient cycling in the Great Lakes over the past several decades. The resurgence of the filamentous green alga Cladophora appears to be one of the consequences of this invasion. Sloughed Cladophora deteriorates water quality, fouls recreational beaches, and may contribute to outbreaks of avian botulism, which have been especially severe in the Sleeping Bear Dunes National Lakeshore (SLBE) region of Lake Michigan. To help determine the fate of sloughed Cladophora, a Lagrangian particle trajectory model was developed to track the transport of Cladophora fragments in the nearshore zone based upon a physical transport-mixing model. The model results demonstrate that the primary deposition sites of sloughed Cladophora within the SLBE region are mid-depth sites not far away from their initial growth area. Because of high algae production in the nearshore waters and limited exchange between the inner and outer bay, the shoreline beach of Platte Bay appears to be particularly vulnerable to fouling, with overall three times as many accumulated particles as those along the Sleeping Bear Bay and Good Harbor Bay. The results of this model may be used to guide regional environmental management initiatives and provide insights into the mechanisms responsible for avian botulism outbreaks. This model may also inform the development of whole-lake ecosystem models that account for nearshore-offshore interactions.

Isolation, identification, and biochemical characterization of a novel bifunctional phosphomannomutase/phosphoglucomutase from the metagenome of the brown alga Laminaria digitata

Macroalgae host diverse epiphytic bacterial communities with potential symbiotic roles including important roles influencing morphogenesis and growth of the host, nutrient exchange, and protection of the host from pathogens. Macroalgal cell wall structures, exudates, and intra-cellular environments possess numerous complex and valuable carbohydrates such as cellulose, hemi-cellulose, mannans, alginates, fucoidans, and laminarin. Bacterial colonizers of macroalgae are important carbon cyclers, acquiring nutrition from living macroalgae and also from decaying macroalgae. Seaweed epiphytic communities are a rich source of diverse carbohydrate-active enzymes which may have useful applications in industrial bioprocessing. With this in mind, we constructed a large insert fosmid clone library from the metagenome of Laminaria digitata (Ochrophyta) in which decay was induced. Subsequent sequencing of a fosmid clone insert revealed the presence of a gene encoding a bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM) enzyme 10L6AlgC, closely related to a protein from the halophilic marine bacterium, Cobetia sp. 10L6AlgC was subsequently heterologously expressed in Escherichia coli and biochemically characterized. The enzyme was found to possess both PMM and PGM activity, which had temperature and pH optima of 45°C and 8.0, respectively; for both activities. The PMM activity had a K m of 2.229 mM and V max of 29.35 mM min-1 mg-1, while the PGM activity had a K m of 0.5314 mM and a V max of 644.7 mM min-1 mg-1. Overall characterization of the enzyme including the above parameters as well as the influence of various divalent cations on these activities revealed that 10L6AlgC has a unique biochemical profile when compared to previously characterized PMM/PGM bifunctional enzymes. Thus 10L6AlgC may find utility in enzyme-based production of biochemicals with different potential industrial applications, in which other bacterial PMM/PGMs have previously been used such as in the production of low-calorie sweeteners in the food industry.

What lies on macroalgal surface: diversity of polysaccharide degraders in culturable epiphytic bacteria

Macroalgal surface constitutes a peculiar ecological niche and an advantageous substratum for microorganisms able to degrade the wide diversity of algal glycans. The degrading enzymatic activities of macroalgal epiphytes are of paramount interest for the industrial by-product sector and biomass resource applications. We characterized the polysaccharide hydrolytic profile of bacterial isolates obtained from three macroalgal species: the red macroalgae Asparagopsis taxiformis and Sphaerococcus coronopifolius (Rhodophyceae) and the brown Halopteris scoparia (Phaeophyceae), sampled in South Portugal. Bacterial enrichment cultures supplemented with chlorinated aliphatic compounds, typically released by marine algae, were established using as inoculum the decaying biomass of the three macroalgae, obtaining a collection of 634 bacterial strains. Although collected from the same site and exposed to the same seawater seeding microbiota, macroalgal cultivable bacterial communities in terms of functional and phylogenetic diversity showed host specificity. Isolates were tested for the hydrolysis of starch, pectin, alginate and agar, exhibiting a different hydrolytic potential according to their host: A. taxiformis showed the highest percentage of active isolates (91%), followed by S. coronopifolius (54%) and H. scoparia (46%). Only 30% of the isolates were able to degrade starch, while the other polymers were degraded by 55-58% of the isolates. Interestingly, several isolates showed promiscuous capacities to hydrolyze more than one polysaccharide. The isolate functional fingerprint was statistically correlated to bacterial phylogeny, host species and enrichment medium. In conclusion, this work depicts macroalgae as holobionts with an associated microbiota of interest for blue biotechnologies, suggesting isolation strategies and bacterial targets for polysaccharidases' discovery.

Enrichment of psychrophilic and acidophilic sulfate-reducing bacterial consortia - a solution toward acid mine drainage treatment in cold regions

Failure of sulfate-reducing bacteria (SRB)-mediated treatment of acid mine drainage (AMD) in cold regions due to inhibition of bacteria by acidic pH and low temperature can be overcome by enriching psychrophilic and acidophilic microbial consortia from local metal-rich sediments. In this study, we enriched microbial consortia from Arctic mine sediments at varying pH (3-7) and temperatures (15-37 °C) under anaerobic conditions with repeated sub-culturing in three successive stages, and analyzed the microbial community using 16S rRNA gene sequencing. The enriched SRB genera resulted in high sulfate reduction (85-88%), and significant metal removal (49-99.9%) during the initial stages (stage 1 and 2). Subsequently, sub-culturing the inoculum at pH 3-4.5 resulted in lower sulfate reduction (9-34%) due to the inhibition of SRB by accumulated acetic acid (0.3-9 mM). The microbial metabolic interactions for successful sulfate and metal removal involved initial glycerol co-fermentation to acetic acid at acidic pH (by Desulfosporosinus, Desulfotomaculum, Desulfurospora, and fermentative bacteria including Cellulomonas and Anaerovorax), followed by acetic acid oxidation to CO₂ and H₂ (by Desulfitobacterium) at neutral pH, and subsequent H₂ utilization (by Desulfosporosinus). The results, including the structural and functional properties of enriched microbial consortia, can inform the development of effective biological treatment strategies for AMD in cold regions.

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

Influence of Filter Pore Size on Composition and Relative Abundance of Bacterial Communities and Select Host-Specific MST Markers in Coastal Waters of Southern Lake Michigan

Water clarity is often the primary guiding factor in determining whether a prefiltration step is needed to increase volumes processed for a range of microbial endpoints. In this study, we evaluate the effect of filter pore size on the bacterial communities detected by 16S rRNA gene sequencing and incidence of two host-specific microbial source tracking (MST) markers in a range of coastal waters from southern Lake Michigan, using two independent data sets collected in 2015 (bacterial communities) and 2016–2017 (MST markers). Water samples were collected from river, shoreline, and offshore areas. For bacterial communities, each sample was filtered through a 5.0-μm filter, followed by filtration through a 0.22-μm filter, resulting in 70 and 143 filter pairs for bacterial communities and MST markers, respectively. Following DNA extraction, the bacterial communities were compared using 16S rRNA gene amplicons of the V3–V4 region sequenced on a MiSeq Illumina platform. Presence of human (Bacteroides HF183) and gull (Gull2, Catellicoccus marimammalium) host-specific MST markers were detected by qPCR. Actinobacteriota, Bacteroidota, and Proteobacteria, collectively represented 96.9% and 93.9% of the relative proportion of all phyla in the 0.22- and 5.0-μm pore size filters, respectively. There were more families detected in the 5.0-μm pore size filter (368) than the 0.22-μm (228). There were significant differences in the number of taxa between the two filter sizes at all levels of taxonomic classification according to linear discriminant analysis (LDA) effect size (LEfSe) with as many as 986 taxa from both filter sizes at LDA effect sizes greater than 2.0. Overall, the Gull2 marker was found in higher abundance on the 5.0-μm filter than 0.22 μm with the reverse pattern for the HF183 marker. This discrepancy could lead to problems with identifying microbial sources of contamination. Collectively, these results highlight the importance of analyzing pre- and final filters for a wide range of microbial endpoints, including host-specific MST markers routinely used in water quality monitoring programs. Analysis of both filters may increase costs but provides more complete genomic data via increased sample volume for characterizing microbial communities in coastal waters.

Sequestration of microfibers and other microplastics by green algae, Cladophora, in the US Great Lakes

Daunting amounts of microplastics are present in surface waters worldwide. A main category of microplastics is synthetic microfibers, which originate from textiles. These microplastics are generated and released in laundering and are discharged by wastewater treatment plants or enter surface waters from other sources. The polymers that constitute many common synthetic microfibers are mostly denser than water, and eventually settle out in aquatic environments. The interaction of these microfibers with submerged aquatic vegetation has not been thoroughly investigated but is potentially an important aquatic sink in surface waters. In the Laurentian Great Lakes, prolific growth of macrophytic Cladophora creates submerged biomass with a large amount of surface area and the potential to collect and concentrate microplastics. To determine the number of synthetic microfibers in Great Lakes Cladophora, samples were collected from Lakes Erie and Michigan at multiple depths in the spring and summer of 2018. After rinsing and processing the algae, associated synthetic microfibers were quantified. The average loads of synthetic microfibers determined from the Lake Erie and Lake Michigan samples were 32,000 per kg (dry weight (dw)) and 34,000 per kg (dw), respectively, 2-4 orders of magnitude greater than loads previously reported in water and sediment. To further explore this sequestration of microplastics, fresh and aged Cladophora were mixed with aqueous mixtures of microfibers or microplastic in the laboratory to simulate pollution events. Microscopic analyses indicated that fresh Cladophora algae readily interacted with microplastics via adsorptive forces and physical entanglement. These interactions mostly cease upon algal senescence, with an expected release of microplastics in benthic sediments. Collectively, these findings suggest that synthetic microfibers are widespread in Cladophora algae and the affinity between microplastics and Cladophora may offer insights for removing microplastic pollution. Macroalgae in the Laurentian Great Lakes contain high loads of synthetic microfibers, both entangled and adsorbed, which likely account for an important fraction of microplastics in these surface waters.

Expanding spectrum of opportunistic Cedecea infections: Current clinical status and multidrug resistance

Members of the bacterial genus Cedecea cause acute infections worldwide in compromised hosts with serious underlying medical conditions. While global reports of Cedecea infections remain sporadic in the medical literature, cases of multidrug-resistant clinical isolates have been documented each year over the past decade, warranting a comprehensive update on this emerging opportunistic pathogen. Here, we review the clinical manifestations, pathogenesis, natural distribution, epidemiology, and antimicrobial resistance of Cedecea species. Acute infection commonly manifests as bacteremia and pneumonia; however, the spectrum of infectious pathologies associated with Cedecea has expanded to include oral and cutaneous ulcers, orbital cellulitis, and peritonitis. The frequency of resistance among reported clinical isolates was highest to ampicillin, cephalothin, cefoxitin, cefazolin, and ceftazidime. Cedecea isolates harboring metallo-β-lactamases exhibited resistance to carbapenems and fourth-generation cephalosporins. Further research is needed to understand the pathogenicity and multidrug resistance of Cedecea species. Appropriate therapeutic management of Cedecea infections depends on antibiotic susceptibility testing because of variable resistance patterns and the enhanced infection risk in vulnerable populations.

Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan

Restoration of degraded aquatic habitats is critical to preserve and maintain ecosystem processes and economic viability. Effective restoration requires contaminant sources identification. Microbial communities are increasingly used to characterize fecal contamination sources. The objective was to determine whether nearshore and adjacent beach bacterial contamination originated from the Grand Calumet River, a highly urbanized aquatic ecosystem, and to determine if there were correlations between pathogens/feces associated bacteria in any of the samples to counts of the pathogen indicator species Escherichia coli. Water samples were collected from the river, river mouth, nearshore, and offshore sites along southern Lake Michigan. Comparisons among communities were made using beta diversity distances (weighted and unweighted Unifrac, and Bray Curtis) and Principal Coordinate Analysis of 16S rRNA gene Illumina sequence data that indicated river bacterial communities differed significantly from the river mouth, nearshore lake, and offshore lake samples. These differences were further supported using Source Tracker software that indicated nearshore lake communities differed significantly from river and offshore samples. Among locations, there was separation by sampling date that was associated with environmental factors (e.g., water and air temperature, water turbidity). Although about half the genera (48.1%) were common to all sampling sites, linear discriminant analysis effect size indicated there were several taxa that differed significantly among sites; there were significant positive correlations of feces-associated genera with E. coli most probable numbers. Results collectively highlight that understanding microbial communities, rather than relying solely on select fecal indicators with uncertain origin, are more useful for developing strategies to restore degraded aquatic habitats.

Microbial Population Changes in Decaying Ascophyllum nodosum Result in Macroalgal-Polysaccharide-Degrading Bacteria with Potential Applicability in Enzyme-Assisted Extraction Technologies

Seaweeds are of significant interest in the food, pharmaceutical, and agricultural industries as they contain several commercially relevant bioactive compounds. Current extraction methods for macroalgal-derived metabolites are, however, problematic due to the complexity of the algal cell wall which hinders extraction efficiencies. The use of advanced extraction methods, such as enzyme-assisted extraction (EAE), which involve the application of commercial algal cell wall degrading enzymes to hydrolyze the cell wall carbohydrate network, are becoming more popular. Ascophyllum nodosum samples were collected from the Irish coast and incubated in artificial seawater for six weeks at three different temperatures (18 °C, 25 °C, and 30 °C) to induce decay. Microbial communities associated with the intact and decaying macroalga were examined using Illumina sequencing and culture-dependent approaches, including the novel ichip device. The bacterial populations associated with the seaweed were observed to change markedly upon decay. Over 800 bacterial isolates cultured from the macroalga were screened for the production of algal cell wall polysaccharidases and a range of species which displayed multiple hydrolytic enzyme activities were identified. Extracts from these enzyme-active bacterial isolates were then used in EAE of phenolics from Fucus vesiculosus and were shown to be more efficient than commercial enzyme preparations in their extraction efficiencies.

High-throughput analysis of the effects of different fish culture methods on antibiotic resistance gene abundances in a lake

Freshwater lakes are important reservoirs for antibiotic resistance genes (ARGs). In this study, we determined the ARG profiles in water samples from Ying Lake, China, using high-throughput quantitative PCR. The high prevalence of ARGs suggested significant pollution with ARGs in the study area, where the ARG diversity and abundance were greater in an area with box-type fish farming than an area with fenced fish farming. Network analysis indicated the widespread co-occurrence of ARGs and mobile genetic elements. cphA-01, blalMP02, and blaCMY202 were identified as adequate indicator genes for estimating the total ARG abundances. Redundancy analysis indicated that changes in the microbial communities caused by variations in the physicochemical parameters with different fish culture methods mainly determined the ARGs in the lake system. Thus, analyzing the factors that affect ARGs provided novel insights into the mechanisms responsible for the maintenance and propagation of ARGs in a lake.

Microfluidic technology for plankton research

Plankton produces numerous chemical compounds used in cosmetics and functional foods. They also play a key role in the carbon budget on the Earth. In a context of global change, it becomes important to understand the physiological response of these microorganisms to changing environmental conditions. Their adaptations and the response to specific environmental conditions are often restricted to a few active cells or individuals in large populations. Using analytical capabilities at the subnanoliter scale, microfluidic technology has also demonstrated a high potential in biological assays. Here, we review recent advances in microfluidic technologies to overcome the current challenges in high content analysis both at population and the single cell level.