scholarly journals Growth arrest in the active rare biosphere

2018 ◽  
Author(s):  
Bela Hausmann ◽  
Claus Pelikan ◽  
Thomas Rattei ◽  
Alexander Loy ◽  
Michael Pester
Keyword(s):  
Metabolic Activity ◽  
Greenhouse Gas Emission ◽  
Peat Soil ◽  
Ecosystem Functions ◽  
Dissimilatory Sulfate Reduction ◽  
Sulfate Reducer ◽  
Prolonged Time ◽  
Rare Biosphere ◽  
Genes Encoding ◽  
Time Periods

AbstractMicrobial diversity in the environment is mainly concealed within the rare biosphere, which is arbitrarily defined as all species with <0.1% relative abundance. While dormancy explains a low-abundance state very well, the cellular mechanisms leading to rare but active microorganisms are not clear. We used environmental systems biology to genomically and metabolically characterize a cosmopolitan sulfate reducer that is of low abundance but highly active in peat soil, where it contributes to counterbalance methane emissions. We obtained a 98%-complete genome of this low-abundance species, Candidatus Desulfosporosinus infrequens, by metagenomics. To test for environmentally relevant metabolic activity of Ca. D. infrequens, anoxic peat soil microcosms were incubated under diverse in situ-like conditions for 36 days and analyzed by metatranscriptomics. Compared to the no-substrate control, transcriptional activity of Ca. D. infrequens increased 56- to 188-fold in incubations with sulfate and acetate, propionate, lactate, or butyrate, revealing a versatile substrate use. Cellular activation was due to a significant overexpression of genes encoding ribosomal proteins, dissimilatory sulfate reduction, and carbon-degradation pathways, but not of genes encoding DNA or cell replication. We show for the first time that a rare biosphere member transcribes metabolic pathways relevant for carbon and sulfur cycling over prolonged time periods while being growth-arrested in its lag phase.SignificanceThe microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat’s biomass. Dormancy or starvation are typically used to explain a low-abundance state. We show that low-abundance microorganisms can be highly metabolically active while being growth-arrested over prolonged time periods. We show that this is true for microbial keystone species, such as a cosmopolitan but low-abundance sulfate reducer in wetlands that is involved in counterbalancing greenhouse gas emission. Our results challenge the central dogmas “metabolic activity translates directly into growth” as well as “low abundance equals little ecosystem impact” and provide an important step forward in understanding rare biosphere members relevant for ecosystem functions.

scholarly journals Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Bela Hausmann ◽  
Claus Pelikan ◽  
Thomas Rattei ◽  
Alexander Loy ◽  
Michael Pester
Keyword(s):  
Transcriptional Activity ◽  
Peat Soil ◽  
Ecosystem Functions ◽  
Rrna Gene ◽  
Growth State ◽  
Sulfate Reducing ◽  
Rare Biosphere ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Zero Growth

ABSTRACT Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize “Candidatus Desulfosporosinus infrequens,” a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of “Ca. Desulfosporosinus infrequens” increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days. IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat’s biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.

Abstract PO-060: Individualized prediction of meningioma recurrence risk over prolonged time periods

2021 ◽  
Author(s):  
Yasin Mamatjan ◽  
Farshad Nassiri ◽  
Mira Salih ◽  
Kenneth Aldape ◽  
Gelareh Zadeh
Keyword(s):  
Recurrence Risk ◽  
Prolonged Time ◽  
Meningioma Recurrence ◽  
Time Periods ◽  
Individualized Prediction

scholarly journals Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

2017 ◽  
Author(s):  
Taylor K Dunivin ◽  
Justine Miller ◽  
Ashley Shade
Keyword(s):  
Coal Seam ◽  
Arsenic Exposure ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Resistant Bacteria ◽  
Rare Biosphere ◽  
Genes Encoding ◽  
Arsenic Resistant Bacteria

Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic arsenic resistant bacteria spanning six genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRG). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRG provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate’s performance given arsenic exposure in situ. Our results suggest that considering taxonomically-linked tolerance and potential for resistance transferability from the rare biosphere will inform strategies for microbiological management and remediation of environmental As and contribute to a larger consideration of As-exposed microbial ecology.

scholarly journals Optimising patient recall of adverse events over prolonged time periods

Trials ◽  
2011 ◽  
Vol 12 (S1) ◽  
Author(s):  
Louise Hiller ◽  
Janet A Dunn ◽  
Helen B Higgins ◽  
Emma Ogburn-Storey ◽  
Shrushma Loi ◽  
...  
Keyword(s):  
Adverse Events ◽  
Prolonged Time ◽  
Patient Recall ◽  
Time Periods

Cerebrovascular disease incidence in workers occupationally exposed to radiation over prolonged time periods

2014 ◽  
Vol 114 (12) ◽  
pp. 128 ◽  
Author(s):  
T. V. Azizova ◽  
M. V. Bannikova ◽  
M. V. Moseeva ◽  
E. S. Grigor'eva ◽  
L. N. Krupenina
Keyword(s):  
Cerebrovascular Disease ◽  
Disease Incidence ◽  
Prolonged Time ◽  
Occupationally Exposed ◽  
Time Periods

scholarly journals Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

2021 ◽  
Author(s):  
Rikuan Zheng ◽  
Ruining Cai ◽  
Rui Liu ◽  
Yeqi Shan ◽  
Ge Liu ◽  
...  
Keyword(s):  
Sulfate Reduction ◽  
Deep Sea ◽  
Phylogenetic Analyses ◽  
Cold Seep ◽  
Sulfur Cycling ◽  
Rrna Gene ◽  
Dissimilatory Sulfate Reduction ◽  
Operational Taxonomic Units ◽  
Deep Sea Sediments ◽  
Genes Encoding

AbstractChloroflexi bacteria are abundant and globally distributed in various unexplored biospheres on Earth. However, only few Chloroflexi members have been cultivated, hampering further understanding of this important group. In the current study, we firstly clarify the high abundance of the phylum Chloroflexi in deep-sea sediments via the operational taxonomic units analysis. We further successfully isolate a novel Chloroflexi strain ZRK33 from cold seep sediments by using an enrichment medium constantly supplemented with rifampicin. Phylogenetic analyses based on 16S rRNA gene, genome, RpoB and EF-tu proteins indicate that strain ZRK33 represents a novel class, and the class is designated as Sulfochloroflexia because whole set of genes encoding key enzymes responsible for assimilatory sulfate reduction are identified in the genome of strain ZRK33. Indeed, assimilation of sulfate or thiosulfate by strain ZRK33 evidently benefits its growth and morphogenesis. Proteomic results suggest that metabolization of sulfate or thiosulfate significantly promotes the transport and degradation of various macromolecules and thereby stimulating the energy production. Notably, the putative genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the metagenome-assembled genomes of 27 Chloroflexi members derived from deep-sea sediments, strongly suggesting that Chloroflexi bacteria play undocumented key roles in deep-sea sulfur cycling.

Which management option has the highest greenhouse gas reduction potential for drained peatlands?

2021 ◽  
Author(s):  
Merit van den Berg ◽  
Christian Fritz ◽  
Bas van de Riet ◽  
Stefan Weideveld ◽  
Thomas Gremmen ◽  
...  
Keyword(s):  
The Netherlands ◽  
Greenhouse Gas ◽  
Greenhouse Gas Emission ◽  
C Sequestration ◽  
Water Levels ◽  
Ecosystem Functions ◽  
Management Options ◽  
Plant Yields ◽  
Oxygen Intrusion ◽  
Almost All

&lt;p&gt;Almost all peatlands in the Netherlands are drained for agricultural purposes or in the past for peat extraction. What remains is a peatland area of about 300.000 ha of which 85 % is used for agriculture. As a result of peat oxidation, these areas are still subsiding by about 1 cm per year. Another effect is the enormous emission of CO&lt;sub&gt;2&lt;/sub&gt;, which contributes to about 4% of total Dutch greenhouse gas emissions. With the awareness of a changing climate and the need for protection against flooding of coastal areas, solutions are being searched to reduce or stop peat oxidation and coinciding land subsidence and CO&lt;sub&gt;2&lt;/sub&gt; emission.&lt;/p&gt;&lt;p&gt;In this presentation we will show different management options (subsoil irrigation, pressurized subsoil irrigation, paludiculture) which are currently being tested in the Netherlands. They will be put into perspective of data from other European studies. These options all focus on increasing the groundwater table to lower oxygen intrusion and consequently lower aerobic decomposition. Depending on crop choices, water levels may need to stay 40 cm below the surface to maximize fodder plant yields, or go to surface level to increase peat ecosystem functions like C-sequestration. The management options range from maintaining the current land-use by elevating summer water levels, with submerged drainage, to the development of peat-forming plant species by complete rewetting. Data of the effects of these management options on CO&lt;sub&gt;2&lt;/sub&gt; emission show that Sphagnum farming is the most promising mitigation option to reduce greenhouse gas emission from drained peatlands. It turned the land from a carbon and greenhouse gas source into a sink.&lt;/p&gt;

The Ecologist and the New Ecology

2016 ◽  
Author(s):  
Oswald J. Schmitz
Keyword(s):  
Environmental Policy ◽  
Protected Areas ◽  
Human Nature ◽  
Ecosystem Functions ◽  
Global Trends ◽  
Sustainability Ethics ◽  
Long Time ◽  
Important Challenge ◽  
Experimental Approaches ◽  
Time Periods

This chapter examines the efforts of ecologists—with the help of the New Ecology—to better understand nature in ecosystems created and heavily populated by humans. Ecology has developed into a science in support of sustaining nature for people. This fresh scientific role is certainly helping to overcome the human–nature divide by promoting the view that biodiversity and ecosystem functions must be protected to provide the suite of environmental services, inside as well as outside of protected areas, in support of humanity. Ecologists are now realizing that understanding and predicting global trends in biodiversity has important implications for sustainability, ethics, and environmental policy in the interest of both humans and nature. An important challenge is to devise new experimental approaches that can speak to issues playing out at the large spatial extents and long time periods that are commensurate with the scales of human engagement with nature.

scholarly journals Effect of trans-Cinnamaldehyde on Methicillin-Resistant Staphylococcus aureus Biofilm Formation: Metabolic Activity Assessment and Analysis of the Biofilm-Associated Genes Expression

2019 ◽  
Vol 21 (1) ◽  
pp. 102 ◽  
Author(s):  
Barbara Kot ◽  
Hubert Sytykiewicz ◽  
Iwona Sprawka ◽  
Małgorzata Witeska
Keyword(s):  
Staphylococcus Aureus ◽  
Metabolic Activity ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Binding Protein ◽  
Expression Level ◽  
Biofilm Inhibition ◽  
Methicillin Resistant ◽  
Fibrinogen Binding ◽  
Genes Encoding ◽  
Laminin Binding Protein

The effects of trans-cinnamaldehyde (TC) on transcriptional profiles of biofilm-associated genes and the metabolic activity of two methicillin-resistant Staphylococcus aureus (MRSA) strains showing a different degree of adherence to polystyrene, were evaluated. Metabolic activity of S. aureus in biofilm was significantly decreased in the presence of TC at 1/2 minimum biofilm inhibition concentration (MBIC). Expression levels of the genes encoding laminin binding protein (eno), elastin binding protein (ebps) and fibrinogen binding protein (fib) in the presence of TC at 1/2 MBIC were lower than in untreated biofilm in both the weakly and strongly adhering strain. The highest decrease of expression level was observed in case of fib in the strongly adhering strain, in which the amount of fib transcript was 10-fold lower compared to biofilm without TC. In the presence of TC at 1/2 MBIC after 3, 6, 8 and 12 h, the expression level of icaA and icaD, that are involved in the biosynthesis of polysaccharide intercellular adhesin, was above half lower in the weakly adhering strain compared to biofilm without TC. In the strongly adhering strain the highest decrease in expression of these genes was observed after 3 and 6 h. This study showed that TC is a promising anti-biofilm agent for use in MRSA biofilm-related infections.

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