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This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

Microbial Ecology 2001: Volume 41 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_2000-11_40_4 . Next issue: sim_microbial-ecology_2001-01_41_1 .

400p. : 23 cm

400p. : 23 cm

Microbial Ecology 1980: Volume 6 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_1979_5_4 . Next issue: sim_microbial-ecology_1980_6_1 .

Microbial Ecology 1990: Volume 20 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_may-june-1990_19_3 . Next issue: sim_microbial-ecology_july-august-1990_20_1 .

Microbial Ecology 2001: Volume 42 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_2001-05_41_4 . Next issue: sim_microbial-ecology_2001-07_42_1 .

Microbial Ecology 2001: Volume 42 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_2001-05_41_4 . Next issue: sim_microbial-ecology_2001-07_42_1 .

Book chapter

This article is from PLoS ONE , volume 8 . Abstract Necrotizing enterocolitis (NEC) is the most devastating intestinal disease affecting preterm infants. In addition to being associated with short term mortality and morbidity, survivors are left with significant long term sequelae. The cost of caring for these infants is high. Epidemiologic evidence suggests that use of antibiotics and type of feeding may cause an intestinal dysbiosis important in the pathogenesis of NEC, but the contribution of specific infectious agents is poorly understood. Fecal samples from preterm infants ≤32 weeks gestation were analyzed using 16S rRNA based methods at 2, 1, and 0 weeks, prior to diagnosis of NEC in 18 NEC cases and 35 controls. Environmental factors such as antibiotic usage, feeding type (human milk versus formula) and location of neonatal intensive care unit (NICU) were also evaluated. Microbiota composition differed between the three neonatal units where we observed differences in antibiotic usage. In NEC cases we observed a higher proportion of Proteobacteria (61%) two weeks and of Actinobacteria (3%) 1 week before diagnosis of NEC compared to controls (19% and 0.4%, respectively) and lower numbers of Bifidobacteria counts and Bacteroidetes proportions in the weeks before NEC diagnosis. In the first fecal samples obtained during week one of life we detected a novel signature sequence, distinct from but matching closest to Klebsiella pneumoniae, that was strongly associated with NEC development later in life. Infants who develop NEC exhibit a different pattern of microbial colonization compared to controls. Antibiotic usage correlated with these differences and combined with type of feeding likely plays a critical role in the development of NEC.

This article is from PLoS ONE , volume 8 . Abstract Necrotizing enterocolitis (NEC) is the most devastating intestinal disease affecting preterm infants. In addition to being associated with short term mortality and morbidity, survivors are left with significant long term sequelae. The cost of caring for these infants is high. Epidemiologic evidence suggests that use of antibiotics and type of feeding may cause an intestinal dysbiosis important in the pathogenesis of NEC, but the contribution of specific infectious agents is poorly understood. Fecal samples from preterm infants ≤32 weeks gestation were analyzed using 16S rRNA based methods at 2, 1, and 0 weeks, prior to diagnosis of NEC in 18 NEC cases and 35 controls. Environmental factors such as antibiotic usage, feeding type (human milk versus formula) and location of neonatal intensive care unit (NICU) were also evaluated. Microbiota composition differed between the three neonatal units where we observed differences in antibiotic usage. In NEC cases we observed a higher proportion of Proteobacteria (61%) two weeks and of Actinobacteria (3%) 1 week before diagnosis of NEC compared to controls (19% and 0.4%, respectively) and lower numbers of Bifidobacteria counts and Bacteroidetes proportions in the weeks before NEC diagnosis. In the first fecal samples obtained during week one of life we detected a novel signature sequence, distinct from but matching closest to Klebsiella pneumoniae, that was strongly associated with NEC development later in life. Infants who develop NEC exhibit a different pattern of microbial colonization compared to controls. Antibiotic usage correlated with these differences and combined with type of feeding likely plays a critical role in the development of NEC.

Tim Otten Seminar for ENVR 400, UNC-CH

Tim Otten Seminar for ENVR 400, UNC-CH

Microbial Ecology 1997: Volume 33 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_november-december-1996_32_3 . Next issue: sim_microbial-ecology_january-february-1997_33_1 .

Microbial Ecology 1999: Volume 38 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_1999-05_37_4 . Next issue: sim_microbial-ecology_1999-07_38_1 .

Microbial Ecology 1999: Volume 38 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_1999-05_37_4 . Next issue: sim_microbial-ecology_1999-07_38_1 .

This article is from Biology Direct , volume 6 . Abstract : A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level.The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice. Reviewers: This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Maureen A. O'Malley.

xv,436p. : 24 cm

Bulletin (West Virginia University. Agricultural Experiment Station)

Microbial Ecology in Health and Disease is an active peer-reviewed academic journal covering research on various human microbial ecosystems and their role in health and disease. It was established in 1988 and is published quarterly by Taylor & Francis. The journal focuses on the study of microbial communities and their interactions with the environment and human health. It covers a wide range of topics related to microbial ecology, including the role of microorganisms in disease pathogenesis, host-microbe interactions, and the impact of microbial communities on ecosystem dynamics. The scope of the journal includes original research articles, reviews, and technical notes that contribute to the understanding of microbial communities' diversity and function. Additionally, it explores the implications of microbial ecology in various fields, such as medicine, agriculture, and environmental science, serving as a platform for sharing advancements in microbial ecology research, including the study of both pathogenic and beneficial microorganisms. The Internet Archive Collection contains microfilm published between 1988 and 1996 Microbial Ecology in Health and Disease can be found online at: www.tandfonline.com/journals/zmeh20 The ISSN is: 0891-060X

Microbial Ecology in Health and Disease is an active peer-reviewed academic journal covering research on various human microbial ecosystems and their role in health and disease. It was established in 1988 and is published quarterly by Taylor & Francis. The journal focuses on the study of microbial communities and their interactions with the environment and human health. It covers a wide range of topics related to microbial ecology, including the role of microorganisms in disease pathogenesis, host-microbe interactions, and the impact of microbial communities on ecosystem dynamics. The scope of the journal includes original research articles, reviews, and technical notes that contribute to the understanding of microbial communities' diversity and function. Additionally, it explores the implications of microbial ecology in various fields, such as medicine, agriculture, and environmental science, serving as a platform for sharing advancements in microbial ecology research, including the study of both pathogenic and beneficial microorganisms. The Internet Archive Collection contains microfilm published between 1988 and 1996 Microbial Ecology in Health and Disease can be found online at: www.tandfonline.com/journals/zmeh20 The ISSN is: 0891-060X

Microbial Ecology in Health and Disease is an active peer-reviewed academic journal covering research on various human microbial ecosystems and their role in health and disease. It was established in 1988 and is published quarterly by Taylor & Francis. The journal focuses on the study of microbial communities and their interactions with the environment and human health. It covers a wide range of topics related to microbial ecology, including the role of microorganisms in disease pathogenesis, host-microbe interactions, and the impact of microbial communities on ecosystem dynamics. The scope of the journal includes original research articles, reviews, and technical notes that contribute to the understanding of microbial communities' diversity and function. Additionally, it explores the implications of microbial ecology in various fields, such as medicine, agriculture, and environmental science, serving as a platform for sharing advancements in microbial ecology research, including the study of both pathogenic and beneficial microorganisms. The Internet Archive Collection contains microfilm published between 1988 and 1996 Microbial Ecology in Health and Disease can be found online at: www.tandfonline.com/journals/zmeh20 The ISSN is: 0891-060X

Microbial Ecology 1991: Volume 21 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_november-december-1990_20_3 . Next issue: sim_microbial-ecology_january-february-1991_21_1 .

Experiments made with cyanobacteria, phototrophic bacteria, and methanogenic bacteria are detailed. Significant carbon isotope fractionation data is included. Taken from well documented extant microbial communities, this data provides a basis of comparison for isotope fractionation values measured in Archean and Proterozoic (preCambrian) rocks. Media, methods, and techniques used to acquire data are also described.

This article is from PLoS ONE , volume 8 . Abstract Due to antimicrobial properties, nisin is one of the most commonly used and investigated bacteriocins for food preservation. Surprisingly, nisin has had limited use in animal feed as well as there are only few reports on its influence on microbial ecology of the gastrointestinal tract (GIT). The present study therefore aimed at investigating effects of dietary nisin on broiler chicken GIT microbial ecology and performance in comparison to salinomycin, the widely used ionophore coccidiostat. In total, 720 one-day-old male Ross 308 chicks were randomly distributed to six experimental groups. The positive control (PC) diet was supplemented with salinomycin (60 mg/kg). The nisin (NI) diets were supplemented with increasing levels (100, 300, 900 and 2700 IU nisin/g, respectively) of the bacteriocin. The negative control (NC) diet contained no additives. At slaughter (35 days of age), activity of specific bacterial enzymes (α- and β-glucosidases, α-galactosidases and β-glucuronidase) in crop, ileum and caeca were significantly higher (P

Microbial Ecology in Health and Disease 1994: Volume 7 , Issue Index. Digitized from IA1643710-04 . Previous issue: sim_microbial-ecology-in-health-and-disease_november-december-1993_6_6 . Next issue: sim_microbial-ecology-in-health-and-disease_1994_7_contents .

This article is from The ISME Journal , volume 8 . Abstract Ribosomal RNA (rRNA) genes are widely utilized in depicting organismal diversity and distribution in a wide range of environments. Although a few cases of lateral transfer of rRNA genes between closely related prokaryotes have been reported, it remains to be reported from eukaryotes. Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genome-walking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two protein-coding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.

Microbial Ecology 1991: Volume 22 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_may-june-1991_21_3 . Next issue: sim_microbial-ecology_july-august-1991_22_1 .

Microbial Ecology in Health and Disease 1993: Volume 6 , Issue CONTENTS. Digitized from IA1643710-04 . Previous issue: sim_microbial-ecology-in-health-and-disease_november-december-1992_5_6 . Next issue: sim_microbial-ecology-in-health-and-disease_january-february-1993_6_1 .

Microbial Ecology in Health and Disease 1993: Volume 6 , Issue CONTENTS. Digitized from IA1643710-04 . Previous issue: sim_microbial-ecology-in-health-and-disease_november-december-1992_5_6 . Next issue: sim_microbial-ecology-in-health-and-disease_january-february-1993_6_1 .

Microbial Ecology is an active publication covering original articles in all areas of ecology involving microorganisms. It was established in 1974 and is published 8 times a year by Springer New York LLC. The periodical features original research articles, review articles, perspectives, and short communications. The scope of the publication covers diverse subjects within microbial ecology, including but not limited to microbial diversity, community structure, microbial interactions, microbial symbiosis, biogeochemical cycles, microbial ecology in different ecosystems, and the impacts of environmental factors on microbial populations. Microbial Ecology can be found online at: https://www.springer.com/journal/248

Microbial Ecology 1985: Volume 11 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_1984-12_10_4 . Next issue: sim_microbial-ecology_1985-03_11_1 .

Microbial Ecology 1985: Volume 11 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_1984-12_10_4 . Next issue: sim_microbial-ecology_1985-03_11_1 .

In this article we describe a multi-week investigative laboratory in microbial ecology/diversity and nitrogen cycling that we have used in our introductory biology course. This module encourages active student involvement in experimental design, using the scientific literature and quantitative analysis of large data sets. Students analyze soil microbial community diversity using EcoPlates (sole source carbon utilization patterns). Also, functional analysis of these communities includes assays for nitrate, nitrite and ammonium to determine experimental effects on the nitrogen cycle. Students are continually assessed by various strategies throughout the module. (Contains 4 tables and 2 figures.)

An essential part of the efficient operation of any microbiology laboratory involved in sample analysis is a standard procedures manual. The purpose of this manual is to provide concise and well defined instructions on routine technical procedures involving sample analysis and methods for monitoring and maintaining quality control within the laboratory. Of equal importance is the safe operation of the laboratory. This manual outlines detailed procedures to be followed in the microbial ecology laboratory to assure safety, analytical control, and validity of results.

This article is from PLoS ONE , volume 9 . Abstract The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.

This article is from PLoS ONE , volume 9 . Abstract The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.

Book chapter

Book chapter

Microbial Ecology 1995: Volume 29 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_november-december-1994_28_3 . Next issue: sim_microbial-ecology_january-february-1995_29_1 .

Microbial Ecology 2002: Volume 44 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_2002-05_43_4 . Next issue: sim_microbial-ecology_2002-07_44_1 .

Microbial Ecology 2002: Volume 44 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_2002-05_43_4 . Next issue: sim_microbial-ecology_2002-07_44_1 .

Microbial Ecology 1992: Volume 23 , Issue Index. Digitized from IA1643634-06 . Previous issue: sim_microbial-ecology_november-december-1991_22_3 . Next issue: sim_microbial-ecology_january-february-1992_23_1 .

Bibl.-Index

Bibl.-Index