scholarly journals Methane-Oxidizing Bacteria in a California Upland Grassland Soil: Diversity and Response to Simulated Global Change

2005 ◽  
Vol 71 (5) ◽  
pp. 2642-2652 ◽  
Author(s):  
Hans-Peter Horz ◽  
Virginia Rich ◽  
Sharon Avrahami ◽  
Brendan J. M. Bohannan
Keyword(s):  
Relative Abundance ◽  
Environmental Changes ◽  
Atmospheric Temperature ◽  
Global Changes ◽  
The Novel ◽  
Type Ii ◽  
Atmospheric Methane ◽  
Antagonistic Interaction ◽  
Methane Oxidizing Bacteria ◽  
Upland Grassland

ABSTRACT We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to “RA 14” or “WB5FH-A,” which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of nonsynonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.

Comparative surface and ultrastructural views of methylotrophic bacteria by TEM, STEM, SE, and freeze-etch electron microscopy.

1987 ◽  
Vol 45 ◽  
pp. 792-793
Author(s):  
T.A. Fassel ◽  
M.J. Schaller ◽  
M.E. Lidstrom ◽  
C.C. Remsen
Keyword(s):  
Cytoplasmic Membrane ◽  
Structural Features ◽  
Methylotrophic Bacteria ◽  
Type I ◽  
Type Ii ◽  
Membrane Complex ◽  
Oxidation Of Methane ◽  
Methane Oxidizing Bacteria ◽  
Wall Structures ◽  
Methylomonas Albus

Methylotrophic bacteria play an Important role in the environment in the oxidation of methane and methanol. Extensive intracytoplasmic membranes (ICM) have been associated with the oxidation processes in methylotrophs and chemolithotrophic bacteria. Classification on the basis of ICM arrangement distinguishes 2 types of methylotrophs. Bundles or vesicular stacks of ICM located away from the cytoplasmic membrane and extending into the cytoplasm are present in Type I methylotrophs. In Type II methylotrophs, the ICM form pairs of peripheral membranes located parallel to the cytoplasmic membrane. Complex cell wall structures of tightly packed cup-shaped subunits have been described in strains of marine and freshwater phototrophic sulfur bacteria and several strains of methane oxidizing bacteria. We examined the ultrastructure of the methylotrophs with particular view of the ICM and surface structural features, between representatives of the Type I Methylomonas albus (BG8), and Type II Methylosinus trichosporium (OB-36).

scholarly journals Demographic history and genomic response to environmental changes in a rapid radiation of wild rats

2021 ◽  
Author(s):  
Deyan Ge ◽  
Anderson Feijó ◽  
Zhixin Wen ◽  
Alexei V Abramov ◽  
Liang Lu ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Demographic History ◽  
Terrestrial Ecosystems ◽  
Tibet Plateau ◽  
Global Changes ◽  
Rapid Radiation ◽  
Protein Functions ◽  
Wild Rats ◽  
Qinghai Tibet Plateau ◽  
Genomic Response

Abstract For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau (QHTP) was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.

scholarly journals Unexpected metabolic versatility among type II methanotrophs in the Alphaproteobacteria

2020 ◽  
Vol 401 (12) ◽  
pp. 1469-1477
Author(s):  
Anna Hakobyan ◽  
Werner Liesack
Keyword(s):  
Global Climate Change ◽  
Global Climate ◽  
Type Ii ◽  
Mixotrophic Growth ◽  
Methane Cycle ◽  
Oxidation Activity ◽  
Methane Oxidizing Bacteria ◽  
Metabolic Versatility ◽  
Carbon Compounds ◽  
Growth Requirement

AbstractAerobic methane-oxidizing bacteria, or methanotrophs, play a crucial role in the global methane cycle. Their methane oxidation activity in various environmental settings has a great mitigation effect on global climate change. Alphaproteobacterial methanotrophs were among the first to be taxonomically characterized, nowadays unified in the Methylocystaceae and Beijerinckiaceae families. Originally thought to have an obligate growth requirement for methane and related one-carbon compounds as a source of carbon and energy, it was later shown that various alphaproteobacterial methanotrophs are facultative, able to grow on multi-carbon compounds such as acetate. Most recently, we expanded our knowledge of the metabolic versatility of alphaproteobacterial methanotrophs. We showed that Methylocystis sp. strain SC2 has the capacity for mixotrophic growth on H2 and CH4. This mini-review will summarize the change in perception from the long-held paradigm of obligate methanotrophy to today’s recognition of alphaproteobacterial methanotrophs as having both facultative and mixotrophic capabilities.

scholarly journals Identification of RISC-Associated Adenoviral MicroRNAs, a Subset of Their Direct Targets, and Global Changes in the Targetome upon Lytic Adenovirus 5 Infection

2014 ◽  
Vol 89 (3) ◽  
pp. 1608-1627 ◽  
Author(s):  
Florian Bellutti ◽  
Maximilian Kauer ◽  
Doris Kneidinger ◽  
Thomas Lion ◽  
Reinhard Klein
Keyword(s):  
Gene Expression ◽  
Relative Abundance ◽  
A549 Cells ◽  
Global Changes ◽  
Cellular Mirnas ◽  
Total Rna ◽  
Cellular Mrnas ◽  
Comprehensive Picture ◽  
Infected Cells ◽  
Adenovirus 5

ABSTRACTAdenoviruses encode a set of highly abundant microRNAs (mivaRNAs), which are generated by Dicer-mediated cleavage of the larger noncoding virus-associated RNAs (VA RNAs) I and II. We performed deep RNA sequencing to thoroughly investigate the relative abundance of individual single strands of mivaRNA isoforms in human A549 cells lytically infected with human adenovirus 5 (Ad5) at physiologically relevant multiplicities of infection (MOIs). In addition, we investigated their relative abundance in the endogenous RNA-induced silencing complexes (RISCs). The occupation of endogenous RISCs by mivaRNAs turned out to be pronounced but not as dominant as previously inferred from experiments with AGO2-overexpressing cells infected at high MOIs. In parallel, levels of RISC-incorporated mRNAs were investigated as well. Analysis of mRNAs enriched in RISCs in Ad5-infected cells revealed that only mRNAs with complementarity to the seed sequences of mivaRNAs derived from VA RNAI but not VA RNAII were overrepresented among them, indicating that only mivaRNAs derived from VA RNAI are likely to contribute substantially to the posttranscriptional downregulation of host gene expression. Furthermore, to generate a comprehensive picture of the entire transcriptome/targetome in lytically infected cells, we determined changes in cellular miRNA levels in both total RNA and RISC RNA as well, and bioinformatical analysis of mRNAs of total RNA/RISC fractions revealed a general, genome-wide trend toward detargeting of cellular mRNAs upon infection. Lastly, we identified the direct targets of both single strands of a VA RNAI-derived mivaRNA that constituted one of the two most abundant isoforms in RISCs of lytically infected A549 cells.IMPORTANCEViral and cellular miRNAs have been recognized as important players in virus-host interactions. This work provides the currently most comprehensive picture of the entire mRNA/miRNA transcriptome and of the complete RISC targetome during lytic adenovirus infection and thus represents the basis for a deeper understanding of the interplay between the virus and the cellular RNA interference machinery. Our data suggest that, at least in the model system that was employed, lytic infection by Ad5 is accompanied by a measurable global net detargeting effect on cellular mRNAs, and analysis of RISC-associated viral small RNAs revealed that the VA RNAs are the only source of virus-encoded miRNAs. Moreover, this work allows to assess the power of individual viral miRNAs to regulate cellular gene expression and provides a list of proven and putative direct targets of these miRNAs, which is of importance, given the fact that information about validated targets of adenovirus-encoded miRNAs is scarce.

scholarly journals The diversity of plankton as bioindicators in Kakap River Estuary, West Kalimantan

DEPIK ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 174-179
Author(s):  
Widadi Padmarsari Soetignya ◽  
Patrisia Marniati ◽  
Mardan Adijaya ◽  
Yunita Magrima Anzani
Keyword(s):  
Relative Abundance ◽  
Environmental Changes ◽  
Diversity Index ◽  
River Estuary ◽  
West Kalimantan ◽  
Abundance And Diversity ◽  
Index Value ◽  
Plankton Diversity ◽  
Research Period

Kakap River Estuary plays an essential role in the life organisms, but it is vulnerable to environmental changes and pollution caused by human activities. This study aims to assess the presence of plankton species, their abundance and diversity as aquatic ecological bio-indicators in Kakap River Estuary. Plankton and water samples were taken for three months, with a frequency of one sample per month, viz. in March, April and June 2020 from four sampling stations in Kakap River Estuary, West Kalimantan. A total of 34 species of plankton were observed from all sampling sites, and identified to belong to 18 classes. Chlorophyceae had the highest relative abundance among the phytoplanktons (40.10%), followed by Bacillariophyceae (21.86%) and Cyanophyceae (19.28%). Oscillatoria sp. and Hydrodictyon sp. were the most dominant phytoplankton species. There were 8 classes of zooplankton identified from all sampling stations throughout the research period. Hexanauplia had the highest relative abundance among the zooplanktons (36.56%) followed by Euglenophyceae (24.37%). The plankton diversity index (H ′) values ranged between 2.33 -3.11. The plankton evenness index value ranged from 0.79 to 0.89 which indicates high plankton evenness at all samping stations, and this is supported by a low dominance index value at all stations ranging from 0.06-0.16. Station 1 had high Shannon-Wienner diversity index score, while for station 2, 3, 4, their scores were in the moderate level. Overall. the diversity index of the plankton from all sampling sites indicated that the quality of the water had no pollution to light pollution level.Keywords:PhytoplanktonZooplanktonWater quality

Methanotrophs and Methanogens in Masonry

1998 ◽  
Vol 64 (11) ◽  
pp. 4530-4532 ◽  
Author(s):  
Martin Kussmaul ◽  
Markus Wilimzig ◽  
Eberhard Bock
Keyword(s):  
Methane Production ◽  
Methanogenic Archaea ◽  
Cell Number ◽  
Type Ii ◽  
Historical Buildings ◽  
Average Cell ◽  
Biogenic Methane ◽  
Methane Oxidizing Bacteria ◽  
Low Concentrations ◽  
Growth Substrates

ABSTRACT Methanotrophs were present in 48 of 225 stone samples which were removed from 19 historical buildings in Germany and Italy. The average cell number of methanotrophs was 20 CFU per g of stone, and their activities ranged between 11 and 42 pmol of CH4 g of stone−1 day−1. Twelve strains of methane-oxidizing bacteria were isolated. They belonged to the type II methanotrophs of the genera Methylocystis,Methylosinus, and Methylobacterium. In masonry, growth substrates like methane or methanol are available in very low concentrations. To determine if methane could be produced by the stone at rates sufficient to support growth of methanotrophs, methane production by stone samples under nonoxic conditions was examined. Methane production of 0.07 to 215 nmol of CH4 g of stone−1 day−1 was detected in 23 of 47 stone samples examined. This indicated the presence of the so-called “mini-methane”-producing bacteria and/or methanogenic archaea. Methanotrophs occurred in nearly all samples which showed methane production. This finding indicated that methanotrophs depend on biogenic methane production in or on stone surfaces of historical buildings.

Long-Term Ecological Research and Evolving Frameworks of Disturbance Ecology

BioScience ◽  
2020 ◽  
Vol 70 (2) ◽  
pp. 141-156 ◽  
Author(s):  
Evelyn E Gaiser ◽  
David M Bell ◽  
Max C N Castorani ◽  
Daniel L Childers ◽  
Peter M Groffman ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Global Environmental Change ◽  
Disturbance Ecology ◽  
Ecological Systems ◽  
Environmental Drivers ◽  
Global Changes ◽  
Ecological Research ◽  
Social Ecological ◽  
Long Term Ecological Research

Abstract Detecting and understanding disturbance is a challenge in ecology that has grown more critical with global environmental change and the emergence of research on social–ecological systems. We identify three areas of research need: developing a flexible framework that incorporates feedback loops between social and ecological systems, anticipating whether a disturbance will change vulnerability to other environmental drivers, and incorporating changes in system sensitivity to disturbance in the face of global changes in environmental drivers. In the present article, we review how discoveries from the US Long Term Ecological Research (LTER) Network have influenced theoretical paradigms in disturbance ecology, and we refine a framework for describing social–ecological disturbance that addresses these three challenges. By operationalizing this framework for seven LTER sites spanning distinct biomes, we show how disturbance can maintain or alter ecosystem state, drive spatial patterns at landscape scales, influence social–ecological interactions, and cause divergent outcomes depending on other environmental changes.

scholarly journals Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Randall R. Jiménez ◽  
Gilbert Alvarado ◽  
José Sandoval ◽  
Simone Sommer
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
Environmental Changes ◽  
Defense Mechanism ◽  
Anthropogenic Activities ◽  
Habitat Disturbance ◽  
Amphibian Declines ◽  
Stress Factors ◽  
Skin Microbiome ◽  
Disturbed Habitats

Abstract Background The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be “extinct” have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd. Results We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance. Conclusions Our findings support the microbial “Anna Karenina principle”, in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.

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