Freshwater Microbiology: Perspectives of Bacterial Dynamics in Lake Ecosystems

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FRESHWATER MICROBIOLOGY
Copyright
List of contributors
Preface
Acknowledgments
1 - Bacterial community composition in lakes
	Introduction
	Historical perspective of lake bacterial communities
	Study of bacteria in lake environments; why is it so important?
	Bacterial biogeography in lakes
	Biodiversity and abundance of bacteria from freshwater lakes
	Bacterial alpha diversity
	Bacterial beta diversity
	Bacterial abundances and spatial patterns
	Bacterial population dynamics
	Diversity-productivity relationship in freshwater bacterial communities
	Microbial dormancy
	Influence of habitat heterogeneity and submerged macrophytes on bacterial community composition in freshwater lakes
		Habitat heterogeneity
		Submerged macrophytes
	Top-down and bottom-up induced shifts in bacterial abundance production and community composition
	Zooplankton and aquatic bacterial linkages in freshwater lakes
	Bacterial community resistance and resilience in lakes
	Novel bacteria from freshwater lake ecosystems
	Case studies of bacterial community of lake ecosystems
	Lake Baikal, Russia
	Dianchi Lake, China
	Lake Tanganyika, Africa
	Yunnan Plateau, China
	Chandra Tal and Dashair Lake, India
	Manasbal Lake, India
	Dal Lake, India
	Gurudongmar Lake, India
	Comparative study of some freshwater lakes in India
	Conclusions
	Acknowledgments
	References
2 - Bacterial diversity of the rock-water interface in freshwater ecosystem
	Introduction
	Sessile bacteria
	Attachment of freshwater bacteria to solid surfaces
	Microbial epilithic and endolithic biofilms
	Microbial dynamics of epilithic mat communities
	Role of epilithic and endolithic microbes
	Colonization pattern of bacterial communities in endolithic habitats
	Epilithic bacteria and mineral formation
	Chemolithotrophic microbial mats on subsurface rocks
	Microbial life in deep granitic rocks
	Identification of lithic bacteria
	Effect of different factors on bacterial attachment to submerged rock surfaces
	Case study
		Bacterial diversity of rock-water interface in Lake Tawani
		Hydrobionts at the water-rock interface in Lake Baikal
		Microorganisms in deep igneous rock aquifers of Finland
	Conclusions
	References
3 - Impact of environmental changes and human activities on bacterial diversity of lakes
	Introduction
	Sources of bacteria in lake water
	Association of lake bacterial diversity with changing environmental features
		Temperature
		Hydrogen ion concentration (pH)
		Salinity
		Total dissolved solids
		Dissolved oxygen
		Alkalinity
		Nitrogen and phosphorus
		Biological oxygen demand
		Chemical oxygen demand
	Human activities and lake bacterial diversity
	Climatic variables and lake bacterial diversity
	Socioeconomic factors and lake bacterial diversity
	Fecal contamination of surface waters
	Advances in aquatic microbial detection and quantification
	Conclusions
	References
4 - Spatio-temporal patterns of bacterial diversity along environmental gradients and bacterial attachment to organic aggregates
	Introduction
	Spatio-temporal distribution of microbial communities
	Drivers of microbial communities in lakes
		Lake bacterial assemblages along the altitudinal gradient
		Lake bacterial assemblages along the latitudinal gradient
		Lake bacterial assemblages along the urban water quality gradient
		Lake bacterial assemblages and microcystis decomposition
	Effect of grazers on bacterial community structure and production in trophic lakes
	Diversity-functioning relationships in lake bacterial communities
	Environmental heterogeneity and diversity-functioning relationship
	Organic aggregates in surface water bodies
	Structural composition of aggregate-associated bacterial communities
	Diversity of organic aggregate–attached bacteria in lakes
		Organic aggregate–associated bacterial communities in deep lakes
		Organic aggregate–associated bacterial communities in shallow eutrophic lakes
		Abundance of organic aggregate–attached bacteria in lakes
		Growth efficiency of organic aggregate–associated bacteria
	Aggregate-associated organic matter and bacterial turnover
	Ecological significance of organic aggregate–attached bacteria
	Conclusions
	References
5 - Metagenomic insights into the diversity and functions of microbial assemblages in lakes
	Introduction
	Metagenomics: historical perspectives
	Sequencing technologies
	Metagenomics of freshwater lakes—basic steps (Fig. 5.1)
		Sample collection and preparation
		DNA extraction
		Amplification and sequencing
		Bioinformatics
			Assembly
			Phylogenetic binning
			Metagenome gene prediction and functional annotation
			Metagenomic data sharing, storage, and management
	Freshwater lakes metagenomic studies
		Freshwater lakes and toxic cyanobacterial blooms
		Freshwater lakes and viral metagenomics
		Freshwater lakes and prokaryotic metagenomics
		Freshwater lakes and antibiotic resistance genes
	Conclusions
	References
6 - Depth distribution of microbial diversity in lakes
	Introduction
	The neuston layer
	Planktonic freshwater prokaryotes
	Phototrophic bacteria
	Sediment layer
	Vertical distribution of sulfate-reducing bacteria
	Vertical distribution of iron-oxidizing bacteria
	Vertical distribution of manganese-oxidizing bacteria
	Vertical distribution of ammonia-oxidizing archaea in lakes
	Case studies
		Lake Pavin and Lake Aydat
		Lake Piburger
		Lake Grosse
		Lake Pavin
		Lonar Lake
		Lake Kivu
		Lake Fryxell
		English Lake district
		Dianchi Lake and Erhai Lake
	Conclusions
	References
	Further reading
7 - Exploring bacterial diversity: from cell to sequence
	Introduction
	Microbial diversity and its importance
	Microbial cell structure
	Bacillus
	Coccus
	Vibrio
	Spirilla
	Structural components of a bacterial cell
		Capsule
		Cell wall
	Plasma membrane
	Cytoplasm
	Surface appendages
		Flagella
		Pili
		Fimbriae
	Bacterial genome
		Plasmids
	Exploring microbial diversity
	Phenotypic approach
	Plate counting
	Community level physiological profiling
	Phospholipid fatty acid analysis
	Fatty acid methyl ester analysis
	Identification of microorganisms using fatty acid methyl ester analysis
	Molecular approach
	Barcodes/molecular markers of microbial world
	16S rRNA gene
	gyrB
	23S rRNA gene
	rpoB
	dnaK
	dsrAB
	16S-23S rDNA ISR
	Molecular tools for exploring microbial diversity
	Polymerase chain reaction
	Basic concept of PCR
	Steps in PCR
	Types of PCR
		Multiplex PCR
		RT-PCR
		qPCR and RT-qPCR
		Touchdown polymerase chain reaction
		Assembly polymerase chain reaction
		Colony polymerase chain reaction
		Nested polymerase chain reaction
	Denature gradient gel electrophoresis (DGGE)
	Terminal restriction fragment length polymorphisms (T-RFLP)
	Single-strand conformation polymorphism
	Amplified ribosomal DNA restriction analysis (ARDRA)
	Fluorescent in situ hybridization
	Clone libraries
	Gel electrophoresis
	Polyacrylamide gel electrophoresis
	Sequencing of DNA
		Sanger sequencing
		Next-generation sequencing
	Conclusions
	References
	Further reading
8 - Bacterial biofilms: the remarkable heterogeneous biological communities and nitrogen fixing microorganisms in lakes
	Introduction
	Availability of biofilms in fresh water systems
	Biofilm diversity
	Biofilm structure
	Biofilm formation
	Biofilm maturation
	Factors influencing bacterial biofilm formation
	Quorum sensing and biofilm development
	General stress response
	Persisters
	Culturing biofilms
		Static microtiter plate assays
		Tube biofilms
		Colony biofilms
		Rotating disk and concentrical cylinder reactors
		Biofilm growth on peg lids
	Methods for characterization of biofilms
		Confocal laser scanning microscopy
		Scanning electron microscopy
		Nuclear magnetic resonance spectroscopy
	Techniques for studying biofilms
		Staining assays
			Crystal violet assay
			DMMB assay
			Fluorescein-di-acetate assay
			Live/dead BacLight assay
		Metabolic assays
			Resazurin assay
			XTT assay
			BioTimer assay
		Genetic assays
			qRT-PCR
			Fluorescence in situ hybridization
	Role of biofilms in bioremediation
	Types of pollutants remediated by biofilms
	Nitrogen fixing microorganisms in lakes
	Conclusions
	References
9 - Microbial diversity in freshwater ecosystems and its industrial potential
	Freshwater lake characteristics
	Microbial diversity of cyanobacteria
	Classification of microalgae and its significance
		Origin of microalgal diversity
			Chlorophyta
			Rhodophyta
			Haptophyta
			Dinophyta
			Eustigmatophyceae
			Bacillariophyceae
			Labyrinthulomycetes
	Biotechnological importance of Cyanobacteria and microalgae
		Cyanobacteria
			Bioremediation by Cyanobacteria
			Fine chemicals from Cyanobacteria
			Pharmaceutical production by Cyanobacteria
			Cyanobacterial bioplastics (polyhydroxyalkanoates, PHAs)
		Microalgae
	Future industrial potentials of Cyanobacteria (blue-green algae) and microalgae
		Hydrogen from Cyanobacteria
		Biodiesel from microalgae
		Bioactive products from microalgae
		Other products from microalgae
		Environmental applications of microalgae
	Industrial processes for microalgae and cyanobacteria
	Conclusions
	References
10 - Bacteria: the natural indicator of environmental pollution
	Introduction
	Air pollution
	Water pollution
	Fresh water pollution
	Marine pollution
	Fecal contamination of fresh and marine waters
	Eutrophication
	Soil and land pollution
	Antibiotic-resistant bacteria as pollution indicators
	Pollutant-specific bacterial indicators
	Conclusions
	Acknowledgments
	References
	Further reading
Index
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