scholarly journals Editorial: Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments

2016 ◽  
Vol 7 ◽  
Author(s):  
Maurizio Labbate ◽  
Justin R. Seymour ◽  
Federico Lauro ◽  
Mark V. Brown
Keyword(s):  
Microbial Ecology ◽  
Anthropogenic Impacts ◽  
Aquatic Environments ◽  
And Function

Regenerative functions and microbial ecology of coral reefs. I. Assays for microbial population

1971 ◽  
Vol 17 (8) ◽  
pp. 1081-1089 ◽  
Author(s):  
L. DiSalvo ◽  
K. Gundersen
Keyword(s):  
Coral Reefs ◽  
Microbial Ecology ◽  
Surface Sediments ◽  
Microbial Population ◽  
Aquatic Environments ◽  
Organic Residue ◽  
Efficient System ◽  
Bacterial Counts ◽  
Kaneohe Bay ◽  
Bacteria And Fungi

Sediments obtained from complex internal reef spaces at Kaneohe Bay, Hawaii, and Eniwetok Atoll, Marshall Is., were apparently homologous to the surface sediments of flat-bottomed aquatic environments. The sediments were heavily populated by bacteria, among which were numerous chitin- and agar-digesting species. Some bacteria and fungi from the reef sediments were capable of digesting a relatively insoluble organic residue obtained from thalli of a calcareous reef alga (Porolilhon sp.). Some elementary analyses of the reef sediments are presented for use in making comparisons of bacterial counts between stations.Arguments are made for the existence of an efficient system of mineralization based on the unique biogenic structure and high organismic diversity of coral reefs.

THE INTERACTIONS OF VERTEBRATES AND INVERTEBRATES IN PEATLANDS AND MARSHES

1987 ◽  
Vol 119 (S140) ◽  
pp. 15-30 ◽  
Author(s):  
Henry R. Murkin ◽  
Bruce D.J. Batt
Keyword(s):  
Current Knowledge ◽  
Life Cycles ◽  
Future Research ◽  
Aquatic Environments ◽  
Research Needs ◽  
Avian Community ◽  
Wide Range ◽  
Dead Plant ◽  
Living Organisms ◽  
And Function

AbstractThis paper reviews the interactions of vertebrates and invertebrates in peatlands and marshes to assess current knowledge and future research needs. Living organisms may interact through a number of direct trophic and nutrient pathways and a variety of non-trophic, habitat-dependent relationships. Freshwater marshes and peatlands are dynamic aquatic environments and organisms that occupy these areas must be adapted to a wide range of environmental conditions. The avian community illustrates the main interactions of invertebrates and vertebrates in peatlands and marshes. Waterfowl, along with fish and furbearers, are the most economically important vertebrates using these habitats. Each of these groups has important trophic and habitat links to the invertebrates within wetlands.The most common interaction between vertebrates and invertebrates is the use of invertebrates as food by vertebrates. Few studies, however, have dealt with trophic dynamics or secondary production within wetlands. Waterfowl, fish, and many other wetland vertebrates, during all or part of their life cycles, regularly feed on invertebrates. Some invertebrates are vectors of disease and parasites to vertebrates. Vertebrates can directly affect the structural substrate that invertebrates depend on as habitat through consumption of macrophytes or through the use of living and dead plant material in the construction of houses and nests. Conversely, herbivorous invertebrates may directly affect the survival and distribution of macrophytes in wetlands. Macrophyte distribution, in turn, is an important factor in determining vertebrate use of wetlands. The general lack of both taxonomic and ecological information on invertebrates in wetlands is the main hindrance to future elucidation of vertebrate–invertebrate interactions in these environments. Development of invertebrate sampling techniques suitable for wetland habitats also is necessary. More specific research needs must be met to develop a better understanding of the structure and function of these dynamic systems.

scholarly journals Methods of Studying Diversity of Bacterial Comunities: A Review

2017 ◽  
Vol 48 (3) ◽  
pp. 154-165
Author(s):  
H. Salmonová ◽  
V. Bunešová
Keyword(s):  
Microbial Ecology ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Molecular Genetic ◽  
Profound Change ◽  
Predominant Component ◽  
And Function

Abstract Bacterial life is a predominant component of all environments, occurring in communities usually of complex diversity. Bacteria are engines of globally important processes which makes them subject of interest to many scientific studies. Although many kinds of methods have been developed and microbial ecology has undergone a profound change in the last two decades with regard to methods employed, the analysis of community composition and function still remains a great challenge. In this article we present an overview of methods commonly used for the study of bacterial diversity. Emphasis was placed on cultivation, biochemical and chemotaxonomic, and molecular-genetic based methods.

scholarly journals Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

Minerals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 596 ◽  
Author(s):  
Shuang Zhou ◽  
Min Gan ◽  
Jianyu Zhu ◽  
Xinxing Liu ◽  
Guanzhou Qiu
Keyword(s):  
Community Structure ◽  
Next Generation Sequencing ◽  
Microbial Ecology ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Structure And Function ◽  
Next Generation ◽  
Sequencing Technologies ◽  
And Function ◽  
Generation Sequencing

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

scholarly journals Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

2021 ◽  
Vol 12 ◽  
Author(s):  
Lauren M. Lui ◽  
Erica L.-W. Majumder ◽  
Heidi J. Smith ◽  
Hans K. Carlson ◽  
Frederick von Netzer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Data Types ◽  
Modeling Framework ◽  
Rapid Acquisition ◽  
Mechanistic Understanding ◽  
And Function

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

scholarly journals Acanthamoeba castellanii Promotes the Survival of Vibrio parahaemolyticus

2008 ◽  
Vol 74 (23) ◽  
pp. 7183-7188 ◽  
Author(s):  
Michelle A. Laskowski-Arce ◽  
Kim Orth
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Acanthamoeba Castellanii ◽  
Survival Advantage ◽  
Aquatic Environments ◽  
Pathogenic Species ◽  
Free Living ◽  
Food Borne ◽  
And Function ◽  
Living Bacteria

ABSTRACT Vibrio parahaemolyticus is a food-borne pathogen that naturally inhabits both marine and estuarine environments. Free-living protozoa exist in similar aquatic environments and function to control bacterial numbers by grazing on free-living bacteria. Protozoa also play an important role in the survival and spread of some pathogenic species of bacteria. We investigated the interaction between the protozoan Acanthamoeba castellanii and the bacterium Vibrio parahaemolyticus. We found that Acanthamoeba castellanii does not prey on Vibrio parahaemolyticus but instead secretes a factor that promotes the survival of Vibrio parahaemolyticus in coculture. These studies suggest that protozoa may provide a survival advantage to an extracellular pathogen in the environment.

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