scholarly journals Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Gareth Trubl ◽  
Jeffrey A. Kimbrel ◽  
Jose Liquet-Gonzalez ◽  
Erin E. Nuccio ◽  
Peter K. Weber ◽  
...  
Keyword(s):  
Carbon Loss ◽  
Peat Soils ◽  
Bacterial Populations ◽  
Anoxic Conditions ◽  
Host Interactions ◽  
Active Virus ◽  
Arctic Soils ◽  
Winter Conditions ◽  
Viral Community ◽  
Freezing Temperatures

Abstract Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

scholarly journals Freshwater Viral Metagenome Reveals Novel and Functional Phage-borne Antibiotic Resistance Genes

2019 ◽  
Author(s):  
Kira Moon ◽  
Ilnam Kang ◽  
Kwang Seung Park ◽  
Jeong Ho Jeon ◽  
Kihyun lee ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Viral Metagenomics ◽  
The Novel ◽  
Multidrug Efflux ◽  
Bacterial Populations ◽  
Host Interactions ◽  
E Coli ◽  
Catalytic Kinetics

Abstract BackgroundAntibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect phylogenetically remote bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate.ResultsWe evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, the novel β-lactamases blaHRV-1 and blaHRVM-1 found in this study had unique sequences, forming distinct clades of Class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages.ConclusionOur results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions.

scholarly journals Active viral population dynamics in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics

2021 ◽  
Author(s):  
Gareth Trubl ◽  
Jeffrey A. Kimbrel ◽  
Jose Liquet-Gonzalez ◽  
Erin E. Nuccio ◽  
Peter K. Weber ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Peat Soil ◽  
Stable Isotope Probing ◽  
Viral Population ◽  
Soil Processes ◽  
Carbohydrate Utilization ◽  
Bacterial Populations ◽  
Viral Ecology ◽  
Bacterial Phyla ◽  
Winter Conditions

AbstractWinter soil processes are critical to the carbon balance of northern ecosystems, yet the microbial ecology governing biogeochemical cycling in frozen soils is largely unknown. We used stable isotope probing targeted metagenomics to reveal the genomic potential of active microbial populations, with an emphasis on viruses, in soils. Peat soils were incubated under simulated winter conditions (subzero and anoxic) with H218O or natural abundance water for 184 and 370 days. Isotope incorporation revealed 46 active bacterial populations (MAGs; spanning 9 bacterial phyla) and 243 active viral populations (vOTUs). Active hosts were predicted for 33% of the active vOTUs and were some of the most abundant MAGs, having capacity for fermentation and carbohydrate utilization. Additionally, almost one-third of vOTUs carried auxiliary metabolic genes spanning five functional categories, highlighting the potential impact of viruses in microbial biogeochemistry. CO2 production throughout the incubation supports our evidence of microbial activities under winter conditions. Our results revealed a multi-trophic and changing microbial community in tandem with a changing viral community targeting dominant active bacteria consistent with the “kill-the-winner” hypothesis. These data have important implications for low-temperature soil processes in northern peatlands and reveal active host-linked soil viral ecology, with potential multifaceted biogeochemical impacts.

Calorimetric assessment of activity in WWTP biomass

2003 ◽  
Vol 48 (3) ◽  
pp. 31-38 ◽  
Author(s):  
E. Daverio
Keyword(s):  
Heat Flux ◽  
Uptake Rate ◽  
Heat Dissipation ◽  
Ammonia Oxidation ◽  
Thermal Response ◽  
Granular Sludge ◽  
Strictly Aerobic ◽  
Bacterial Populations ◽  
Anoxic Conditions ◽  
Rate Test

A heat flux bench-scale calorimeter (Bio-RC1) has been used to assess the metabolic activity of microbial populations involved in wastewater treatment biological processes under aerobic, anoxic and anaerobic conditions. Under strictly aerobic conditions, a linear correlation was observed between oxygen uptake rate and heat flux for heterotrophic and nitrifying bacterial populations. Using the same calorimetric approach and the same apparatus, toxicity and biodegradability of a pesticides factory wastewater were investigated. The activity of heterotrophic and nitrifying aerobic communities was monitored considering both oxygen consumption and heat dissipation, whereas, under anoxic conditions, calorimetric data were compared to the traditional NUR (nitrate uptake rate) test. Heterotrophic activity was found to be 52% inhibited after toxic wastewater exposure under both aerobic and anoxic conditions and 30% inhibition was observed on autotrophic ammonia oxidation. Additionally, calorimetric measurements have been successfully applied to investigate anaerobic digestion. The thermal response of a mesophilic granular sludge to repetitive glucose pulses has been evaluated and a toxicity test has been performed by exposing the biomass to increasing concentrations of formaldehyde.

scholarly journals Estimation of Carbon Stock in the Peat Soils of Bangladesh

2019 ◽  
Vol 45 (1) ◽  
pp. 127-136
Author(s):  
MJ Uddin ◽  
ASM Mohiuddin
Keyword(s):  
Climate Change ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Carbon Stock ◽  
Agricultural Intensification ◽  
Carbon Stocks ◽  
Carbon Loss ◽  
Peat Soils ◽  
Local Stakeholders ◽  
Agricultural Use

There are a very few study on the estimation of carbon stocks in the peat soils of Bangladesh. There are three categories of peat soils in Bangladesh: Sapric peat, Hemic peat and Fibric peat. A study was conducted in these three kinds of peat soils at 100 cm depths regarding their stock. The study shows that the carbon in peat soils is about 0.12 Pg whereas it was about 0.25 Pg during 1970s. So, it was found that soil organic carbon loss is alarming and it has been reduced by half during 50 years of agricultural intensification in Bangladesh. These peat soils are losing their carbon due to the decrease of inundation level by climate change, intensive agricultural use and even fuel use for cooking purposes by the local stakeholders. So, it is very much urgent to take steps in preserving the peat soils of Bangladesh. Asiat. Soc. Bangladesh, Sci. 45(1): 127-136, June 2019

scholarly journals Rotavirus Infection and Cytopathogenesis in Human Biliary Organoids Potentially Recapitulate Biliary Atresia Development

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Sunrui Chen ◽  
Pengfei Li ◽  
Yining Wang ◽  
Yuebang Yin ◽  
Petra E. de Ruiter ◽  
...  
Keyword(s):  
Biliary Atresia ◽  
Neutralizing Antibodies ◽  
Causal Relation ◽  
Morphological Changes ◽  
Fetal Liver ◽  
Three Dimensional ◽  
Neutralizing Antibody ◽  
Rotavirus Infection ◽  
Host Interactions ◽  
Active Virus

ABSTRACT Biliary atresia (BA) is a neonatal liver disease characterized by progressive fibroinflammatory obliteration of both intrahepatic and extrahepatic bile ducts. The etiologies of BA remain largely unknown, but rotavirus infection has been implicated at least for a subset of patients, and this causal relation has been well demonstrated in mouse models. In this study, we aim to further consolidate this evidence in human biliary organoids. We obtained seven batches of human biliary organoids cultured from fetal liver, adult liver, and bile duct tissues. We found that these organoids are highly susceptible and support the full life cycle of rotavirus infection in three-dimensional culture. The robust infection triggers active virus-host interactions, including interferon-based host defense mechanisms and injury responses. We have observed direct cytopathogenesis in organoids upon rotavirus infection, which may partially recapitulate the development of BA. Importantly, we have demonstrated the efficacy of mycophenolic acid and interferon alpha but not ribavirin in inhibiting rotavirus in biliary organoids. Furthermore, neutralizing antibody targeting rotavirus VP7 protein effectively inhibits infection in organoids. Thus, we have substantiated the causal evidence of rotavirus inducing BA in humans and provided potential strategies to combat the disease. IMPORTANCE There is substantial evidence indicating the possible involvement of rotavirus in biliary atresia (BA) development, at least in a subset of patients, but concrete proof remains lacking. In a mouse model, it has been well demonstrated that rotavirus can infect the biliary epithelium to cause biliary inflammation and obstruction, representing the pathogenesis of BA in humans. By using recently developed organoids technology, we now have demonstrated that human biliary organoids are susceptible to rotavirus infection, and this provokes active virus-host interactions and causes severe cytopathogenesis. Thus, our model recapitulates some essential aspects of BA development. Furthermore, we have demonstrated that antiviral drugs and neutralizing antibodies are capable of counteracting the infection and BA-like morphological changes, suggesting their potential for mitigating BA in patients.

scholarly journals Quorum Sensing and Metabolic State of the Host Control Lysogeny-Lysis Switch of Bacteriophage T1

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Leanid Laganenka ◽  
Timur Sander ◽  
Alexander Lagonenko ◽  
Yu Chen ◽  
Hannes Link ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Bacterial Population ◽  
Lytic Cycle ◽  
Receptor Protein ◽  
Lytic Phage ◽  
Camp Receptor Protein ◽  
Metabolic State ◽  
Bacterial Populations ◽  
Host Interactions ◽  
Camp Receptor

ABSTRACT Bacterial viruses, or bacteriophages, are highly abundant in the biosphere and have a major impact on microbial populations. Many examples of phage interactions with their hosts, including establishment of dormant lysogenic and active lytic states, have been characterized at the level of the individual cell. However, much less is known about the dependence of these interactions on host metabolism and signal exchange within bacterial communities. In this report, we describe a lysogenic state of the enterobacterial phage T1, previously known as a classical lytic phage, and characterize the underlying regulatory circuitry. We show that the transition from lysogeny to lysis depends on bacterial population density, perceived via interspecies autoinducer 2. Lysis is further controlled by the metabolic state of the cell, mediated by the cyclic-3′,5′-AMP (cAMP) receptor protein (CRP) of the host. We hypothesize that such combinations of cell density and metabolic sensing may be common in phage-host interactions. IMPORTANCE The dynamics of microbial communities are heavily shaped by bacterium-bacteriophage interactions. But despite the apparent importance of bacteriophages, our understanding of the mechanisms controlling phage dynamics in bacterial populations, and particularly of the differences between the decisions that are made in the dormant lysogenic and active lytic states, remains limited. In this report, we show that enterobacterial phage T1, previously described as a lytic phage, is able to undergo lysogeny. We further demonstrate that the lysogeny-to-lysis decision occurs in response to changes in the density of the bacterial population, mediated by interspecies quorum-sensing signal AI-2, and in the metabolic state of the cell, mediated by cAMP receptor protein. We hypothesize that this strategy enables the phage to maximize its chances of self-amplification and spreading in bacterial population upon induction of the lytic cycle and that it might be common in phage-host interactions.

Carbon loss estimates from cultivated peat soils in Norway: a comparison of three methods

2008 ◽  
Vol 81 (2) ◽  
pp. 157-167 ◽  
Author(s):  
Arne Grønlund ◽  
Atle Hauge ◽  
Anders Hovde ◽  
Daniel P. Rasse
Keyword(s):  
Carbon Loss ◽  
Peat Soils

Non-host interactions to detect anti-Fusarium substances

Planta Medica ◽  
2011 ◽  
Vol 77 (12) ◽  
Author(s):  
O Schumpp ◽  
N Bruderhofer ◽  
K Gindro ◽  
J Wolfender
Keyword(s):  
Host Interactions

COUNTING TOTAL BACTERIA IN LAND ORGANIC WASTE HOUSEHOLD AND LAND INORGANIC WITH TOTAL PLATE COUNT METHOD (TPC)

2017 ◽  
Vol 4 (2) ◽  
pp. 87-91
Author(s):  
Ekamaida Ekamaida
Keyword(s):  
Soil Fertility ◽  
Bacterial Population ◽  
Organic Soil ◽  
Biological Properties ◽  
Plate Count ◽  
Bacterial Populations ◽  
Fertility Data ◽  
Plate Count Method ◽  
The Mean ◽  
Total Bacteria

The soil fertility aspect is characterized by the good biological properties of the soil. One important element of the soil biological properties is the bacterial population present in it. This research was conducted in the laboratory of Microbiology University of Malikussaleh in the May until June 2016. This study aims to determine the number of bacterial populations in soil organic and inorganic so that can be used as an indicator to know the level of soil fertility. Data analysis was done by T-Test that is by comparing the mean of observation parameter to each soil sample. The sampling method used is a composite method, which combines 9 of soil samples taken from 9 sample points on the same plot diagonally both on organic soil and inorganic soil. The results showed the highest bacterial population was found in total organic soil cfu 180500000 and total inorganic soil cfu 62.500.000

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