Next-generation sequencing and culture-based techniques offer complementary insights into fungi and prokaryotes in beach sands

Abstract

• Beach sands represent reservoirs for a variety of bacterial, fungal, and protozoan pathogens. 1 • Epidemiological studies and monitoring efforts have only recently been explored to protect public health. 1 • Current monitoring efforts are based on culture-based enumeration of fecal indicator bacteria and selected fungal pathogens. 2 • Next-generation sequencing (NGS) methods are increasingly being used to more completely characterize microbial communities in sands. 3 • Taken together, NGS and conventional methods can be used in a tool-box approach to better assess health risks. 4 We hypothesized that NGS and culture-based methods would identify the same, predominant taxa in beach sands: Culture-based methods will show greater sensitivity to lowabundance potential pathogens  NGS will offer more extensive characterization of the community and identify novel targets for monitoring efforts

Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations

“…They are different in that the Chao1 estimator gives greater weight to low abundance species (species with less than 10 individuals in a sample), while the ACE estimator gives greater weight to species sample coverage (species with more than 10 individuals in a sample) (Kim et al 2017). In this study, however, both estimators still showed high bacterial species richness in all beach sand samples, as also observed in other beach sand samples (Mudryk et al 2013;Romão et al 2017). This confirms earlier findings that beach sands are microhabitats teaming with microbial life (Sabino et al 2014;Whitman et al 2014;Solo-Gabriele et al 2015).…”

“…Therefore, understanding the microbial community structure and biodiversity of beach sand is useful for assessing the ecological health of the beach sand, as higher biodiversity usually confers better resistance and resilience against environmental perturbation and contamination (Cui et al 2013). The dominance of bacteria belonging to the phyla Proteobacteria, Bacteroidetes, Planctomycetes, Actinobacteria, and Gemmatimonadetes in beach sands has earlier been documented in coastal beach samples (Zheng et al 2014;Romão et al 2017). This may indicate that these phyla have evolved to be the main indigenous bacterial communities in coastal intertidal zones.…”

The Beach Aquifer Microbiome: Research Gaps and Data Needs

“…In intertidal sands, a few studies have characterized the diversity of microbes associated with several potential metabolic functions, as well as potential human pathogens (Yamahara et al, 2007;Cui et al, 2013;Staley and Sadowsky, 2016;Romão et al, 2017). In these studies, the intertidal sands FIGURE 2 | Geographic locations of globally sampled beach aquifers.…”

Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China

“…Furthermore, the indigenous microbial sand communities are also one of the most critical factors for preventing the colonization of harmful exogenous microorganisms, such as fecal indicator bacteria and pathogens, on beach sands [5,6]. Thus, increasing attention is being paid to the biogeographic distribution pattern of sand microbial communities and its driving forces [2,4,[7][8][9]. The importance of environmental filtering in shaping the assembly of sand microbial communities has highlighted, and a significant body of literature has demonstrated, that the distance from shoreline, sand grain size, moisture, temperature, nutrients (including organic and inorganic matters), and chemical contaminants are major environmental factors shaping sand microbial communities [2,7,8,10,11].…”