Geology topics

Satoshi Ishii

Publications and source records attributed to Satoshi Ishii.

5 recordsLinked to original sources

USGS2019

Great Lakes Cladophora harbors phylogenetically diverse nitrogen-fixing microorganims

Abstract Nitrogen‐fixing microorganisms are among the epiphytic communities in Cladophora, potentially benefitting the algae in nutrient‐deficient waters, but their abundance and diversity remain unexplored. In this study, we determined the abundance and taxonomic composition of these nitrogen‐fixing microorganisms in Cladophora growing on rocks, breakwall structures, or submerged dreissenid mussel beds around southern Lake Michigan (N = 33) during the summer 2015, using two complementary genomic techniques: quantitative PCR (qPCR) and shotgun metagenomic sequencing. Genomic DNA was extracted from processed algal pellets, and the nitrogen‐fixing microbes were quantified by qPCR by targeting the nifH gene. Mean nifH concentrations (log10 copy numbers/gram algae fresh weight ± SE) were 5.54 ± 0.09, ranging from 4.31 to 6.57. Mean nifH concentrations in water samples (log10 copy numbers/milliliter of water ± SE) were: 3.25 ± 0.06, ranging from 2.41 to 3.90. Shotgun sequencing of a subset of algal samples representing the four sampling locations (N = 10) revealed as many as 267 nifH reads from among the sequences of the 10 shotgun metagenomes (averaging 27 reads per metagenome), ranging from 5 to 91 reads from Jeorse Park (September) and North Beach (September) locations. Taxonomic assignment of nifH sequences identified members from bacteria and archaea domains showing a clear separation of reads at domain and lower taxonomic levels. Bacteria were relatively more abundant than archaea. Anabaena, Bradyrhizobium, Geobacter, Methylocystis, Oscillatoria sp., and Skermanella (all bacteria), and Methanoregula, Methanothrix, and Methanosarcina (archaea) were among the nitrogen‐fixing genera identified by the MEGAN Community Edition program. Collectively, these findings show that phylogenetically diverse nitrogen‐fixing microbial communities are part of the Cladophora microbiome, likely contributing to the algal nitrogen needs.

Environmental DNA↗

USGS2017

Environmental Escherichia coli : Ecology and public health implications - A review

Escherichia coli is classified as a rod-shaped, Gram-negative bacterium in the family Enterobacteriaceae . The bacterium mainly inhabits the lower intestinal tract of warm-blooded animals, including humans, and is often discharged into the environment through feces or wastewater effluent. The presence of E. coli in environmental waters has long been considered as an indicator of recent fecal pollution. However, numerous recent studies have reported that some specific strains of E. coli can survive for long periods of time, and potentially reproduce, in extra-intestinal environments. This indicates that E. coli can be integrated into indigenous microbial communities in the environment. This naturalization phenomenon calls into question the reliability of E. coli as a fecal indicator bacterium (FIB). Recently, many studies reported that E. coli populations in the environment are affected by ambient environmental conditions affecting their long-term survival. Large-scale studies of population genetics provide the diversity and complexity of E. coli strains in various environments, affected by multiple environmental factors. This review examines the current knowledge on the ecology of E. coli strains in various environments in regards to its role as a FIB and as a naturalized member of indigenous microbial communities. Special emphasis is given on the growth of pathogenic E. coli in the environment, and the population genetics of environmental members of the genus Escherichia . The impact of environmental E. coli on water quality and public health is also discussed.

Journal of Applied Microbiology↗

USGS2017

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

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum , the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90 days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24 h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora , including Acinetobacter , Enterobacter , Kluyvera , Cedecea , and others. In contrast, there were no or very few sequences (< 0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

Great Lakes↗

USGS2015

Application of a microfluidic quantitative polymerase chain reaction technique to monitor bacterial pathogens in beach water and complex environmental matrices

Microfluidic quantitative polymerase chain reaction (MFQPCR) and conventional quantitative polymerase chain reaction methods were compared side by side in detecting and quantifying 19 genetic markers associated with Escherichia coli and select bacterial pathogens in algae, beach sand, and water from Lake Michigan. Enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli , Salmonella spp., Campylobacter jejuni , and Clostridium perfringens were among the pathogens tested. Of the pathogenic markers, eaeA that encodes intimin in EPEC was detected in all sample types: water (5%), detached/floating algae (42%), exposed/stranded algae (43%), sand below exposed algae (27%), and nearshore sand with no algae (22%). Other pathogenic markers, however, were detected sporadically. Despite comparable results from the two methods for the genetic markers tested in this study, the MFQPCR method may be superior, with the advantage of detecting and quantifying multiple pathogens simultaneously in environmental matrices.

Indiana↗

USGS2011

Environmental sources of fecal bacteria

This chapter provides a review of the research on environmental occurrences of faecal indicator bacteria in a variety of terrestrial and aquatic habitats under different geographic and climatic conditions, and discusses how these external sources may affect surface water quality.

Book chapter↗