Books: 'Bacterial communities'

1

Klepac-Ceraj, Vanja. Diversity and phylogenetic structure of two complex marine microbial communities. Ft. Belvoir: Defense Technical Information Center, 2004.

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2

Microbiology, American Society for, ed. Oral microbial communities: Genomic inquiry and interspecies communication. Washington, DC: ASM Press, 2011.

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3

Nyberg, Karin. Impact of organic waste residues on structure and function of soil bacterial communities with emphasis on ammonia oxidizing bacteria. Uppsala: Swedish University of Agricultural Sciences, 2006.

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4

D, Allsopp, Colwell Rita R. 1934-, and Hawksworth D. L, eds. Microbial diversity and ecosystem function: Proceedings of the IUBS/IUMS workshop held at Egham, UK, 10-13 August 1993 in support of the IUBS/UNESCO/SCOPE "DIVERSITAS" programme. Wallingford, Oxon, UK: CAB International, in association with United Nations Environment Programme, 1995.

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5

Santelli, Cara M. Promotion of Mn(II) oxidation and remediation of coal mine drainage in passive treatment systems by diverse fungal and bacterial communities. [Washington]: American Society for Microbiology, 2010.

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6

Exploring denitrifying communities in the environment. Uppsala: Swedish University of Agricultural Sciences, 2006.

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7

Rosenberg, Eugene. The Prokaryotes: Prokaryotic Communities and Ecophysiology. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013.

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8

Braddock, Joan F. Petroleum hydrocarbon-degrading microbial communities in Beaufort-Chukchi Sea sediments. Fairbanks, AK: Coastal Marine Institute, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2004.

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9

Braddock, Joan F. Petroleum hydrocarbon-degrading microbial communities in Beaufort-Chukchi Sea sediments. Fairbanks, AK: Coastal Marine Institute, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2004.

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10

Polar microbiology: The ecology, biodiversity, and bioremediation potential of microorganisms in extremely cold environments. Boca Raton: Taylor & Francis, 2010.

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11

Kato, Sakura Y. Archaea: Structure, habitats, and ecological significance. Hauppauge, N.Y: Nova Science Publishers, 2010.

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12

Levén, Lotta. Anaerobic digestion at mesophilic and thermophilic temperature: With emphasis on degradation of phenols and structures of microbial communities. Uppsala: Swedish University of Agricultural Sciences, 2006.

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13

Genetic Diversity of Soil Bacterial Communities. MDPI, 2020. http://dx.doi.org/10.3390/books978-3-03943-744-3.

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14

Kolenbrander, Paul E. Oral Microbial Communities: Genomic Inquiry and Interspecies Communication. Wiley & Sons, Limited, John, 2014.

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15

(Editor), D. Allsopp, D. L. Hawksworth (Editor), and R. R. Colwell (Editor), eds. Microbial Diversity and Ecosystem Function (Cabi Publishing). CABI, 1996.

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16

Bittleston, Leonora S. Commensals of Nepenthes pitchers. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0023.

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Carnivorous Nepenthes pitcher plants contain aquatic ecosystems within each fluid-filled pitcher. Communities of arthropods and microbes colonize pitcher pools, and some organisms are endemic to the pitcher habitat. Flies and mites are the most apparent colonizers, and together with numerous protists, fungi, and bacteria, they form a food web of predators, decomposers, and primary producers. Bacterial diversity and composition are correlated strongly with fluid pH. Closely related organisms co-occur within pitchers, suggesting that competition is not the primary structuring force of pitcher communities. Pitchers are ephemeral habitats when compared with surrounding soil, and the former communities have fewer organisms and are less predictable than the latter. It is still unknown to what extent pitcher plants and their inhabitants influence one another’s fitness.

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17

Patterson, DJ, and MA Burford. Guide to Protozoa of Marine Aquaculture Ponds. CSIRO Publishing, 2001. http://dx.doi.org/10.1071/9780643101081.

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As well as being a culture environment for fish and crustaceans, an aquaculture pond is a rich and complex ecosystem that is dominated by the microbial community. The community is nourished by food and sunlight, and is made up of algae, bacteria and, importantly, protozoa. Protozoa live by eating other organisms and detritus, or by absorbing soluble organic matter dissolved in the water. Ultimately they affect water quality in aquaculture ponds, including the stability of algal and bacterial communities, and nutrient concentrations. In addition, some protozoa can have adverse effects on the health of cultured species. Guide to Protozoa of Marine Aquaculture Ponds is designed to provide a simple means of identifying the main groups of protozoa found in aquaculture ponds through the use of photographs and drawings. This is supplemented with information on the likely effects of protozoa on water quality and the health of the cultured species. This guide is an indispensable tool for those involved in rearing marine animals, as well as aquaculture researchers and teachers. Please note that this book is spiral-bound.

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18

Kirchman, David L. The ecology of viruses. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0010.

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In addition to grazing, another form of top-down control of microbes is lysis by viruses. Every organism in the biosphere is probably infected by at least one virus, but the most common viruses are thought to be those that infect bacteria. Viruses come in many varieties, but the simplest is a form of nucleic acid wrapped in a protein coat. The form of nucleic acid can be virtually any type of RNA or DNA, single or double stranded. Few viruses in nature can be identified by traditional methods because their hosts cannot be grown in the laboratory. Direct count methods have found that viruses are very abundant, being about ten-fold more abundant than bacteria, but the ratio of viruses to bacteria varies greatly. Viruses are thought to account for about 50% of bacterial mortality but the percentage varies from zero to 100%, depending on the environment and time. In addition to viruses of bacteria and cyanobacteria, microbial ecologists have examined viruses of algae and the possibility that viral lysis ends phytoplankton blooms. Viruses infecting fungi do not appear to lyse their host and are transmitted from one fungus to another without being released into the external environment. While viral lysis and grazing are both top-down controls on microbial growth, they differ in several crucial respects. Unlike grazers, which often completely oxidize prey organic material to carbon dioxide and inorganic nutrients, viral lysis releases the organic material from hosts more or less without modification. Perhaps even more important, viruses may facilitate the exchange of genetic material from one host to another. Metagenomic approaches have been used to explore viral diversity and the dynamics of virus communities in natural environments.

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19

Kirchman, David L. Community structure of microbes in natural environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0004.

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Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.

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20

Meet Your Bacteria: The Hidden Communities That Live in Your Gut and Other Organs. Firefly Books, Limited, 2018.

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21

Kirchman, David L. Microbial growth, biomass production, and controls. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0008.

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Soon after the discovery that bacteria are abundant in natural environments, the question arose as to whether or not they were active. Although the plate count method suggested that they were dormant if not dead, other methods indicated that a large fraction of bacteria and fungi are active, as discussed in this chapter. It goes on to discuss fundamental equations for exponential growth and logistic growth, and it describes phases of growth in batch cultures, continuous cultures, and chemostats. In contrast with measuring growth in laboratory cultures, it is difficult to measure in natural environments for complex communities with co-occurring mortality. Among many methods that have been suggested over the years, the most common one for bacteria is the leucine approach, while for fungi it is the acetate-in ergosterol method. These methods indicate that the growth rate of the bulk community is on the order of days for bacteria in their natural environment. It is faster in aquatic habitats than in soils, and bacteria grow faster than fungi in soils. But bulk rates for bacteria appear to be slower than those for phytoplankton. All of these rates for natural communities are much slower than rates measured for most microbes in the laboratory. Rates in subsurface environments hundreds of meters from light-driven primary production and high organic carbon conditions are even lower. Rates vary greatly among microbial taxa, according to data on 16S rRNA. Copiotrophic bacteria grow much faster than oligotrophic bacteria, but may have low growth rates when conditions turn unfavorable. Some of the factors limiting heterotrophic bacteria and fungi include temperature and inorganic nutrients, but the supply of organic compounds is perhaps most important in most environments.

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22

Atlas, Ronald M., Asim K. Bej, and Jackie Aislabie. Polar Microbiology: The Ecology, Biodiversity and Bioremediation Potential of Microorganisms in Extremely Cold Environments. Taylor & Francis Group, 2009.

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23

Atlas, Ronald M., Asim K. Bej, and Jackie Aislabie. Polar Microbiology. Taylor & Francis Group, 2019.

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24

Atlas, Ronald M., Asim K. Bej, and Jackie Aislabie. Polar Microbiology: The Ecology, Biodiversity and Bioremediation Potential of Microorganisms in Extremely Cold Environments. Taylor & Francis Group, 2009.

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25

Bej, Asim K. Polar Microbiology: The Ecology, Biodiversity and Bioremediation Potential of Microorganisms in Extremely Cold Environments. Taylor & Francis Group, 2010.

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26

Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors. Taylor & Francis Group, 2018.

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27

Gautam, Susma Bhattarai. Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors. Taylor & Francis Group, 2018.

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28

Gautam, Susma Bhattarai. Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors. Taylor & Francis Group, 2018.

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29

Gautam, Susma Bhattarai. Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors. Taylor & Francis Group, 2018.

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30

Northern Gulf of Mexico chemosynthetic ecosystems study: Literature review and data synthesis. New Orleans: U.S. Dept. of the Interior, Minerals Management Service, Gulf of Mexico OCS Region, 1992.

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31

Miller, Thomas E., William E. Bradshaw, and Christina M. Holzapfel. Pitcher-plant communities as model systems for addressing fundamental questions in ecology and evolution. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0024.

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Carnivorous plants have close associations with other species that live in or on the plant. Sarracenia purpurea has a particularly large number of inquiline species, many of which are obligates that live in its water-filled leaves. These include a well-studied food web of bacteria, protozoa, rotifers, mites, and Diptera larvae, all of which depend on the prey of the host plant. This model system has been used to address fundamental questions in ecology and evolution, including studies of keystone predation, succession, consumer versus resource control, invasion, dispersal, and the roles of resources and predators in metacommunities. The microecosystem also has been used to understand density-dependent selection, the genetic structure of populations, evolution over climatic gradients, and evolution in a multispecies, community context. In this chapter, the ecology of this potentially mutualistic contained community is explored in the context of its carnivorous host.

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32

Breidahl, Harry. Dark Secrets: Life Without Sunlight (Life in Strange Places). Chelsea House Publications, 2001.

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33

Sirová, Dagmara, Jiří Bárta, Jakub Borovec, and Jaroslav Vrba. The Utricularia-associated microbiome: composition, function, and ecology. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0025.

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This chapter reviews current advances regarding plant–microbe interactions in aquatic Utricularia. New findings on the composition and function of trap commensals, based mainly on the advances in molecular methods, are presented in the context of the ecological role of Utricularia-associated microorganisms. Bacteria, fungi, algae, and protozoa colonize the Utricularia trap lumen and form diverse, interactive communities. The involvement of these microbial food webs in the regeneration of nutrients from complex organic matter is explained and their potential contribution to the nutrient acquisition in aquatic Utricularia is discussed. The Utricularia–commensal system is suggested to be a suitable model system for studying plant-microbe and microbe-microbe interactions and related ecological questions.

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34

Sheppard, Charles R. C., Simon K. Davy, Graham M. Pilling, and Nicholas A. J. Graham. Microbial, microalgal and planktonic reef life. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198787341.003.0005.

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Microbes, including bacteria, archaea, viruses, fungi, protozoans and microalgae, are the most abundant and arguably the most important members of coral reef communities. They occur in the water column and sediment, and in association with other reef organisms. This chapter describes the abundance, diversity, function and productivity of microbes, with an emphasis on free-living types. They are key to recycling and retention of organic matter via the ‘microbial loop’, and are an important food source for larger reef organisms. The metazoan zooplankton are also described, including larvae of most reef invertebrates and fish. They are described in terms of their duration in the plankton, their settlement behaviour (e.g. that of coral larvae), their daily migration patterns and their role as a food source for larger organisms. Their importance for inter-reef connectivity is discussed.

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35

Kirchman, David L. Predation and protists. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0009.

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Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.

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Books on the topic 'Bacterial communities'

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