Search Results (18)

Despite being low-resource environments, sandy beaches can contain diverse bacterial assemblages. In this study we examined the spatial heterogeneity of bacterial communities in sand on a beach on the Mississippi Gulf Coast, USA. 16S ribosomal RNA gene sequencing was used to characterize bacterial communities in surface sand along 10 m transects from dry sand towards the upper beach to fully submerged sand, as well as up to 0.4 m deep into the sand. There were clear gradients in bacterial community structure based on position on the beach and depth, and community richness and diversity was greater in moist sand subject to tidal influence than drier sand. Bacterial communities in sand higher up the beach were characterized by members of the phyla Bacillota and Actinomycetota, whereas there was an increased presence of picocyanobacteria (phylum Cyanobacteriota) in sand closer to the water and greater diversity overall. Along with gradients in community structure, microbial activity also showed spatial patterns, with microbial extracellular enzyme activity being greatest in surface sand at intermediate positions along the beach transects that were subject to tidal influences but not fully submerged. This research supports the idea of beaches containing diverse bacterial communities and demonstrates that the existence of gradients in beach environments means that these communities show clear patterns in their spatial distribution. Full article

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial communities inhabiting supralittoral–intertidal sediments of two contrasting sandy beaches in the Tadjoura Gulf (Djibouti Republic): Sagallou-Kalaf (SK, rural, siliceous sand) and Siesta Plage (SP, urban, calcareous sand). Sand samples were collected at low tide along 10 m transects perpendicular to the shoreline. Bacterial communities differed significantly between sites and along the sea-to-land gradient, suggesting an influence from both anthropogenic activity and sediment granulometry. SK was dominated by Escherichia-Shigella, Staphylococcus, and Bifidobacterium, associated with human and agricultural sources. SP showed higher richness, with enriched marine-associated genera such as Hoeflea, Xanthomarina, and Marinobacter, also linked to hydrocarbon degradation. Fungal diversity was less variable, but showed significant shifts along transects. SK communities were dominated by Kluyveromyces and Candida, while SP hosted a broader fungal assemblage, including Pichia, Rhodotorula, and Aureobasidium. The higher richness at SP suggests that calcium-rich sands, possibly due to their buffering capacity and greater moisture retention, offer more favorable conditions for microbial colonization. Full article

Exposure to antibiotic-resistant microbial communities in coastal waters is an important threat to human health. Through a ten-year coastal time series, we used metagenomics from 236 time points to provide a comprehensive understanding of the seawater resistome, temporal distribution, and factors influencing frequencies of specific resistance types. Here, we predicted that antibiotic resistance gene frequencies would increase during the winter due to increased rainfall, with terrestrial and enteric taxa serving as the primary carriers of resistance genes in coastal waters. We found that seasonal and interannual trends of antibiotic resistance genes vary by gene and the taxa carrying them, as opposed to a general increase in most resistance genes during specific seasons. However, we found that precipitation and Enterococcus levels may be accurate indicators for total antibiotic resistance gene levels in Newport Beach coastal water. Resistance genes were primarily carried by marine taxa, though some terrestrial taxa and opportunistic pathogens also harbored these genes. Non-marine taxa can be introduced through rain, human activity, or sewage spills. By using metagenomics, we were able to elucidate the antibiotic-resistant bacterial communities in Newport Beach coastal water and demonstrate both seasonal and multiannual trends in their abundance with important implications for local health and safety. Full article

We investigated the presence of the fecal indicator bacteria Escherichia coli, and other taxa associated with sewage communities in coastal sediments, near beaches with reported poor bathing water quality, focusing on the influence of effluent from a local wastewater treatment plant (WWTP) and combined sewer overflows (CSO). Using a three-year dataset, we found that treated wastewater effluent is a significant source of sewage-associated taxa and viable E. coli in the sediments and that no seasonal differences were observed between spring and summer samples. CSO events have a local and temporary effect on the microbial community of sediments, distinct from that of treated wastewater effluent. Sediments affected by CSO had higher abundances of families Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae. Sewage releases may also impact the natural community of the sediments, as higher abundances of marine sulfur-cycling bacteria were noticed in locations where sewage taxa were also abundant. Microbial contamination at locations distant from known CSO and treatment plant outlets suggests additional sources, such as stormwater. This study highlights that while coastal sediments can be a reservoir of E. coli and contain sewage-associated taxa, their distribution and potential origins are complex and are likely not linked to a single source. Full article

Seaweed is a valuable natural resource, but drift or beach-cast seaweed is considered a waste product. Although seaweed is traditionally used as an organic amendment, vermicomposting has the potential to transform the material into valuable organic fertilizer, thereby enhancing its microbial properties. This study aimed to investigate the dynamics of the taxonomic and functional bacterial communities in seaweed during the vermicomposting process by high-throughput sequencing of 16S rRNA gene amplicons. Vermicomposting changed the composition of the bacterial communities, as indicated by the low proportion of bacterial taxa common to the bacterial communities in the raw seaweed and vermicompost (21 to 56 ASVs from more than 900 ASVs per sample type). The observed increase in taxonomic diversity (32% mean increase across sampling times) also affected the functionality of the bacterial communities present in the vermicompost. The diverse bacterial community showed enriched functional pathways related to soil health and plant growth, including the synthesis of antibiotics, amino acids, and phytohormones, as well as the degradation of bisphenol. In conclusion, in terms of microbial load and diversity, vermicompost derived from seaweed is a more valuable organic fertiliser than seaweed itself. Full article

The Vibrio bacteria known to cause infections to humans and wildlife have been largely overlooked in coastal environments affected by beach wrack accumulations from seaweed or seagrasses. This study presents findings on the presence and distribution of potentially pathogenic Vibrio species on coastal beaches that are used for recreation and are affected by red-algae-dominated wrack. Using species-specific primers and 16S rRNA gene amplicon sequencing, we identified V. vulnificus, V. cholerae (non-toxigenic), and V. alginolyticus, along with 14 operational taxonomic units (OTUs) belonging to the Vibrio genus in such an environment. V. vulnificus and V. cholerae were most frequently found in water at wrack accumulation sites and within the wrack itself compared to sites without wrack. Several OTUs were exclusive to wrack accumulation sites. For the abundance and presence of V. vulnificus and the presence of V. cholerae, the most important factors in the water were the proportion of V. fucoides in the wrack, chl-a, and CDOM. Specific Vibrio OTUs correlated with salinity, water temperature, cryptophyte, and blue-green algae concentrations. To better understand the role of wrack accumulations in Vibrio abundance and community composition, future research should include different degradation stages of wrack, evaluate the link with nutrient release, and investigate microbial food-web interactions within such ecosystems, focusing on potentially pathogenic Vibrio species that could be harmful both for humans and wildlife. Full article

Cupressus gigantea is an endangered species mainly distributed on beach land, down-slope, and middle-slope positions along the Yarlung Zangbo River on the Tibet Plateau of China, with an altitude ranging from 3000 to 3400 m. We investigated the rhizosphere and fine root microbiomes of C. gigantea at these three slope positions through metagenomic analysis. Slope positions had a greater influence on microbiome composition in the rhizosphere than that in the fine roots. Down- and middle-slope positions presented higher microbial richness indeces and community similarity, while a more complex co-occurrence network was observed in the beach land samples. Rhizosphere bacterial community assembly was determined via deterministic processes in the beach land and via stochastic processes in the down- and middle-slope positions. Archaeal and fungal community assemblies were both dominated by stochastic processes in the rhizosphere and fine roots at the three slope positions. Nitrogen (N) functional genes were more sensitive to changes in slope positions than phosphorus (N) functional genes. Soil properties explained more than 60% and 34% of the variations in the N and P functional genes and more than 30% and 10% of the variations in the microbiomes in the rhizosphere and fine roots, respectively. Variation in the microbiome was significantly driven by total nirtogen, total potassium, pH, and soil moisture in rhizosphere, and by pH and soil moisture in fine roots. Our observations suggest that the effect of slope position on the microbiomes of C. gigantea was greater for the rhizosphere than the fine roots, with down- and middle-slope positions presenting higher community similarity. Full article

The occurrence and spread of antibiotic resistance have become a pressing global health concern. Understanding the genetic elements that facilitate the dissemination of antibiotic resistance genes (ARGs) in marine environments is crucial for effective microbial surveillance and management strategies. This study aimed to reveal the presence of mobilizable multiresistance clusters, consisting of ARGs associated with mobile genetic elements (MGEs), in marine bacterial communities. Water samples were collected from two beaches in Jeju, South Korea, and screened to identify multi-drug resistant bacteria. A total of 20 bacterial isolates were selected for whole genome sequencing, and through comprehensive genomic analysis, we identified and characterized nine such clusters primarily composed of betalactams, aminoglycosides, and tetracycline ARGs associated with MGEs like IS6, IS9, and Tn3. Additionally, an extensive analysis of 900 marine bacterial genomes from the National Center for Biotechnology Information (NCBI) database was conducted to gain a broader perspective. Our results provide valuable insights into the prevalence and diversity of mobilizable multiresistance clusters in marine bacterial communities. Full article

Balanced fear supports human rational decision-making and useful behavioral responses. In contrast, overwhelming, persistent, and unbalanced fear can paralyze the individual and result in heightened anxiety, lack of cognitive flexibility, fear-based public compliance and serious mental health issues. Psychobiotics research has established that a healthy microbiome is required for balanced fear and mental health protection via control of fear extinction. The recent COVID-19 pandemic featured daily, persistent, fear-of-a-single-contagion conditioning on a global scale paired with various behavioral mandates (e.g., lockdowns of the healthy, required wearing of face masks in many locations including schools, isolation from environmental microbes and each other through the closure of beaches and parks, and restrictions on social gatherings including access to family members in hospitals and senior-assisted facilities). Such mandates degraded the human microbiome and isolated us from each other and useful environmental microbes. It also ignored the historic role of secondary bacterial pathogens in pandemic deaths. This narrative review examines how the institutional promotion of fear-of-a-single-contagion, lack of balanced risk communication, and appalling disregard of our fundamental nature (as majority-microbial human superorganisms) resulted in problems rather than solutions. This review illustrates that government-public health-media promotion of pervasive fear and microbiome-degrading behaviors: (1) increased public compliance, (2) reduced cognitive flexibility, and (3) increased risk of mental health conditions. However, a portion of the general public chose a healthier path through their increased consumption of microbiome- and immune-supportive supplements and fermented foods during and after the COVID-19 pandemic. For a healthier future, public health must follow the lead of this population to ensure that human freedom, rather than paralyzing fear, dominates our future. Full article

Soil proteinase and proteinase-producing microbial community are closely associated with soil fertility and soil health. Sea rice has been planted in the coastal beach of Jiaozhou Bay, China, in an effort to transform saline-alkali soil into arable land. However, the knowledge regarding the bacterial degradation of organic nitrogen in sea rice soils is limited. This study aims to investigate the physicochemical characteristics and enzymatic activities of the sea rice soils, as well as the microbial communities by both the Illumina sequencing-based culture-independent technology and culture-dependent methods. Sea rice soils exhibited a lower salinity and higher organic matter content and proteinase activity, as well as an increase in both the richness and diversity of the proteinase-producing bacterial community, compared to the adjacent non-rice soils. The Proteobacteria phylum and the Gammaproteobacteria class were dominant in sea rice soils, showing higher abundance than in the reference soils. The Planococcus genus and Bacillus-like bacterial communities were abundant in the cultivable proteinase-producing bacteria isolated from sea rice soils. Furthermore, a significant proportion of the extracellular proteinase produced by the isolated soil bacteria consisted of serine proteinases and metalloproteinases. These findings provided new insights into the degradation of soil organic nitrogen in coastal agricultural regions. Full article

The Tijuana River watershed is binational, flowing from Tijuana, Mexico into San Diego and Imperial Beach, USA. Aging sewage and stormwater infrastructure in Tijuana has not kept pace with population growth, causing overflows into this watershed during major rainfall or equipment failures. The public health consequences of this impaired watershed on the surrounding communities remain unknown. Here, we performed untargeted metagenomic sequencing to better characterize the sewage contamination in the Tijuana River, identifying potential pathogens and molecular indicators of antibiotic resistance in surface waters. In 2019–2020, water samples were collected within 48 h of major rainfall events at five transborder flow sites and at the mouth of the river in the US portion of the Tijuana River and estuary. After filtration, DNA was extracted and sequenced, and sequences were run through the Kaiju taxonomic classification program. A pathogen profile of the most abundant disease-causing microbes and viruses present in each of the samples was constructed, and specific markers of fecal contamination were identified and linked to each site. Results from diversity analysis between the sites showed clear distinction as well as similarities between sites and dates, and antibiotic-resistant genes were found at each site. This serves as a baseline characterization of microbial exposures to these local communities. Full article

Beach safety regulation is based on faecal indicators in water, leaving out sand and fungi, whose presence in both matrices has often been reported. To study the abundance, diversity and possible fluctuations of mycobiota, fungi from sand and seawater were isolated from the Portorož beach (Slovenia) during a 1-year period. Sand analyses yielded 64 species of 43 genera, whereas seawater samples yielded 29 species of 18 genera. Environmental and taxonomical data of fungal communities were analysed using machine learning approaches. Changes in the air and water temperature, sunshine hours, humidity and precipitation, air pressure and wind speed appeared to affect mycobiota. The core genera Aphanoascus, Aspergillus, Fusarium, Bisifusarium, Penicillium, Talaromyces, and Rhizopus were found to compose a stable community within sand, although their presence and abundance fluctuated along with weather changes. Aspergillus spp. were the most abundant and thus tested against nine antimycotics using Sensititre Yeast One kit. Aspergillus niger and A. welwitschiae isolates were found to be resistant to amphotericin B. Additionally, four possible human pollution indicators were isolated during the bathing season, including Meyerozyma, which can be used in beach microbial regulation. Our findings provide the foundations for additional research on sand and seawater mycobiota and show the potential effect of global warming and extreme weather events on fungi in sand and sea. Full article

Dalian Jinshitan beach was chosen to evaluate the impact of a typhoon on the bacterial community structure and water quality of a marine bathing beach. The concentration of enterococci was determined by the cultivation method. The bacterial community structure and abundance were analyzed using the 16S rDNA next-generation sequencing and qPCR methods. Results showed that the abundance of cultivable enterococci both in alongshore and offshore seawater increased, while it decreased in dry, wet and submerged sand. The water quality deteriorated immediately after the typhoon, and nearly recovered one month after the typhoon. The typhoon event also decreased the bacterial abundance and changed the bacterial community of the beach. Sphingomonadaceae and Rhodobacteraceae significantly increased in seawater and decreased in dry sand immediately after the typhoon. Human and other fecal taxa increased in water and sand. One month after the typhoon, the diversity and many dominant bacterial taxa nearly recovered in seawater and wet sand. Our work shows that the typhoon changed the bacterial dynamics, deteriorated the water quality and proved the transportation of bacterial taxa and input of fecal pollution between water and beach sand or land. Apart from the impact of the typhoon, the geographical location was another important factor in the changed bacterial community. Full article

The spread of fecal pollutants and antibiotic resistance in the aquatic environment represents a major public health concern and is predicted to increase in light of climate change consequences and the increasing human population pressure on the lagoon and coastal areas. The city of Venice (Italy) is affected by diverse microbial pollution sources, including domestic wastewaters that, due to the lack of modern sewage treatment infrastructure in the historical city center, are released into canals. The outflowing jets of its tidal inlets thus represent a source of contamination for the nearby beaches on the barrier island separating the lagoon from the sea. Metagenomic analyses of DNA extracted from sediment samples from six sites in the canals of the city’s historic center were undertaken to characterize the microbial community composition, the presence of fecal microbes as well as other non-enteric pathogens, and the content of genes related to antibiotic (AB) and heavy metal (HM) resistance, and virulence. The six sites hosted similar prokaryotic communities, although variations in community composition likely related to oxygen availability were observed. All sites displayed relatively high levels of fecal contamination, including the presence of Fecal Indicator Bacteria, sewage- and alternative feces-associated bacteria. Relatively high levels of other potential pathogens were also found. About 1 in 500 genes identified at these sites are related to AB and HM resistance; conversely, genes related to virulence were rare. Our data suggest the existence of widespread sediment microbial pollution in the canals of Venice, coupled with the prevalence of ARGs to antibiotics frequently used in humans as well as of HMRGs to toxic metals that still persists in the lagoon. All of this evidence raises concerns about the consequences on the water quality of the lagoon and adjacent marine areas and the potential risks for humans, deserving further studies. Full article

Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM. Full article