On the role of cave-soil in the carbon cycle. A fist approach.

Karsts cover up to 25 % of the land surface and contain significant sedimentary deposits that become active cave-soils. Subterranean karst ecosystems play an active role in the global carbon cycle in terms of their contribution to the global GHG balance. They act alternately as a source or sink of CO2 and as a rapid sink of CH4. The most recent results indicate that microbiota must play a significant ecological role in the biogeochemical processes that control the subterranean atmosphere composition. Soils forming underneath the surface must host a large part of the subterranean microbiota. But to date, their behaviour concerning the production of gases and exchange with the &#8220;confined troposphere&#8221; has not been evaluated. Systematic direct estimates of CO2 and CH4 fluxes from cave-soils do not exist in literature. And they are needed before global generalizations can be made about the carbon budgets (emissions and sinks) of karstic ecosystems.Here we present pioneering research to evaluate the carbon fluxes from the cave soils directly exchanged with the cave atmosphere. This preliminary study is the first approach to systematically characterize the role of cave-soils in the production and transport of CO2 and CH4 in the subterranean environment. We carried out automatic in situ and real-time monitoring of CO2 and CH4 diffusive fluxes from a sedimentary alluvial soil in Pindal cave for one year (north Spain). We developed seasonal campaigns for CH4 and CO2 fluxes daily continuous monitoring by a LICOR closed chamber-based gas exchange system, in conjunction with a compatible Gasmet FTIR gas analyser. Moreover, autonomous equipment monitored the main micro-environmental parameters of the local subsurface-soil-atmosphere system. To interpret gas exchange processes and rates, and to understand the underlying mechanisms in soils, we also carried out seasonal &#948;13C geochemical tracing by using Picarro cavity ring-down spectroscopy, through simultaneous cave atmosphere-soil-chamber air samplings. We also characterized the soil microbial communities related to the carbon cycle by meta-barcoding analyses of bacterial 16S rRNA genes and Shotgun Metagenomics.Preliminary results show net CO2 emissions from cave-soil on a daily scale, resulting from respiration by chemotrophic microorganisms. We detect significant magnitude variations along the day, reaching occasionally values close to zero. This is remarkable in such thermo-hygrometric stable environment and absence of light. Changes in the cave ventilation regime seems to be the determining factor just in some cases. Intrinsic microbial processes appear to be decisive in others. The results also reveal net CH4 uptake from cave-soil on a daily scale, with no significant magnitude variations along the day. It seems to be linked to the metabolism of Nitrate-dependent methanotrophs belonging to the phylum Rokubacteria. Additionally, we detected significant variations in magnitude and different flow patterns in the cave-soils colonized by biofilms, most prominent in the case of moonmilk deposits.These preliminary results confirm that cave-soil is playing an outstanding role in the processes of production, consumption and storage of CO2 and CH4 and may be partially determining the strong variations of these major GHGs in natural subterranean ecosystems.

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Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

mBio ◽

10.1128/mbio.00569-12 ◽

2013 ◽

Vol 4 (3) ◽

Cited By ~ 64

Author(s):

Daniel P. R. Herlemann ◽

Daniel Lundin ◽

Matthias Labrenz ◽

Klaus Jürgens ◽

Zongli Zheng ◽

...

Keyword(s):

16S Rrna ◽

Carbon Cycle ◽

Baltic Sea ◽

Glycoside Hydrolases ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sulfated Polysaccharides ◽

The Baltic Sea ◽

The Baltic

ABSTRACTThe verrucomicrobial subdivision 2 classSpartobacteriais one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of theSpartobacteriais one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within theSpartobacteriaexists. Since no aquatic representative from theSpartobacteriahas been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic SeaSpartobacteriaphylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype’s distribution within the Baltic Sea indicate a connection toCyanobacteriathat may be the main source of the polysaccharide substrates.IMPORTANCEThe ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the classSpartobacteriawithin theVerrucomicrobiathat, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquaticVerrucomicrobiaby applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able toin silicoisolate genome fragments belonging to a phylotype of theSpartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs withCyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.

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Role of Broiler Carcasses and Processing Plant Air in Contamination of Modified-Atmosphere-Packaged Broiler Products with Psychrotrophic Lactic Acid Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.01644-06 ◽

2006 ◽

Vol 73 (4) ◽

pp. 1136-1145 ◽

Cited By ~ 55

Author(s):

Elina Vihavainen ◽

Hanna-Saara Lundstrï¿½m ◽

Tuija Susiluoto ◽

Joanna Koort ◽

Lars Paulin ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

16S Rrna Genes ◽

Rrna Genes ◽

23S Rrna ◽

Processing Plant ◽

Modified Atmosphere ◽

Production Plant ◽

Meat Spoilage

ABSTRACT Some psychrotrophic lactic acid bacteria (LAB) are specific meat spoilage organisms in modified-atmosphere-packaged (MAP), cold-stored meat products. To determine if incoming broilers or the production plant environment is a source of spoilage LAB, a total of 86, 122, and 447 LAB isolates from broiler carcasses, production plant air, and MAP broiler products, respectively, were characterized using a library of HindIII restriction fragment length polymorphism (RFLP) patterns of the 16 and 23S rRNA genes as operational taxonomic units in numerical analyses. Six hundred thirteen LAB isolates from the total of 655 clustered in 29 groups considered to be species specific. Sixty-four percent of product isolates clustered either with Carnobacterium divergens or with Carnobacterium maltaromaticum type strains. The third major product-associated cluster (17% of isolates) was formed by unknown LAB. Representative strains from these three clusters were analyzed for the phylogeny of their 16S rRNA genes. This analysis verified that the two largest RFLP clusters consisted of carnobacteria and showed that the unknown LAB group consisted of Lactococcus spp. No product-associated LAB were detected in broiler carcasses sampled at the beginning of slaughter, whereas carnobacteria and lactococci, along with some other specific meat spoilage LAB, were recovered from processing plant air at many sites. This study reveals that incoming broiler chickens are not major sources of psychrotrophic spoilage LAB, whereas the detection of these organisms from the air of the processing environment highlights the role of processing facilities as sources of LAB contamination.

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Coaggregation among Nonflocculating Bacteria Isolated from Activated Sludge

Applied and Environmental Microbiology ◽

10.1128/aem.69.10.6056-6063.2003 ◽

2003 ◽

Vol 69 (10) ◽

pp. 6056-6063 ◽

Cited By ~ 91

Author(s):

Anushree Malik ◽

Masashi Sakamoto ◽

Shohei Hanazaki ◽

Masamitsu Osawa ◽

Takanori Suzuki ◽

...

Keyword(s):

16S Rrna ◽

Activated Sludge ◽

Aggregate Size ◽

Spectrophotometric Assay ◽

Full Length ◽

16S Rrna Genes ◽

Rrna Genes ◽

Acinetobacter Junii ◽

Acinetobacter Johnsonii

ABSTRACT Thirty-two strains of nonflocculating bacteria isolated from sewage-activated sludge were tested by a spectrophotometric assay for their ability to coaggregate with one other in two-membered systems. Among these strains, eight showed significant (74 to 99%) coaggregation with Acinetobacter johnsonii S35 while only four strains coaggregated, to a lesser extent (43 to 65%), with Acinetobacter junii S33. The extent and pattern of coaggregation as well as the aggregate size showed good correlation with cellular characteristics of the coaggregating partners. These strains were identified by sequencing of full-length 16S rRNA genes. A. johnsonii S35 could coaggregate with strains of several genera, such as Oligotropha carboxidovorans, Microbacterium esteraromaticum, and Xanthomonas spp. The role of Acinetobacter isolates as bridging organisms in multigeneric coaggregates is indicated. This investigation revealed the role of much-neglected nonflocculating bacteria in floc formation in activated sludge.

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The Xylella fastidiosa-Resistant Olive Cultivar “Leccino” Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS)

Pathogens ◽

10.3390/pathogens9010035 ◽

2019 ◽

Vol 9 (1) ◽

pp. 35 ◽

Cited By ~ 7

Author(s):

Marzia Vergine ◽

Joana B. Meyer ◽

Massimiliano Cardinale ◽

Erika Sabella ◽

Martin Hartmann ◽

...

Keyword(s):

Xylella Fastidiosa ◽

Resistance Mechanisms ◽

16S Rrna Genes ◽

Rrna Genes ◽

Olive Cultivar ◽

Olive Quick Decline Syndrome ◽

Olive Trees ◽

Potential Interactions ◽

Highly Virulent

Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar “Leccino” was compared to the susceptible cultivar “Cellina di Nardò”, in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. “Cellina di Nardò” showed a drastic dysbiosis after X. fastidiosa infection, while “Leccino” (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all “Leccino” and Xf-uninfected “Cellina di Nardò” trees, whereas Ammoniphilus prevailed in Xf-infected “Cellina di Nardò”. Diversity of microbiota in Xf-uninfected “Leccino” was higher than in Xf-uninfected “Cellina di Nardò”. Several bacterial taxa specifically associated with “Leccino” showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of “Leccino” to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.

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Wastewater Irrigation Increases the Abundance of Potentially Harmful Gammaproteobacteria in Soils in Mezquital Valley, Mexico

Applied and Environmental Microbiology ◽

10.1128/aem.01295-14 ◽

2014 ◽

Vol 80 (17) ◽

pp. 5282-5291 ◽

Cited By ~ 42

Author(s):

Melanie Broszat ◽

Heiko Nacke ◽

Ronja Blasi ◽

Christina Siebe ◽

Johannes Huebner ◽

...

Keyword(s):

16S Rrna ◽

Rainy Season ◽

Soil Microbial Communities ◽

Wastewater Irrigation ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

Resistance Determinants ◽

Oxacillin Resistance ◽

Irrigated Soils

ABSTRACTWastewater contains large amounts of pharmaceuticals, pathogens, and antimicrobial resistance determinants. Only a little is known about the dissemination of resistance determinants and changes in soil microbial communities affected by wastewater irrigation. Community DNAs from Mezquital Valley soils under irrigation with untreated wastewater for 0 to 100 years were analyzed by quantitative real-time PCR for the presence ofsulgenes, encoding resistance to sulfonamides. Amplicon sequencing of bacterial 16S rRNA genes from community DNAs from soils irrigated for 0, 8, 10, 85, and 100 years was performed and revealed a 14% increase of the relative abundance ofProteobacteriain rainy season soils and a 26.7% increase in dry season soils for soils irrigated for 100 years with wastewater. In particular,Gammaproteobacteria, including potential pathogens, such asPseudomonas,Stenotrophomonas, andAcinetobacterspp., were found in wastewater-irrigated fields. 16S rRNA gene sequencing of 96 isolates from soils irrigated with wastewater for 100 years (48 from dry and 48 from rainy season soils) revealed that 46% were affiliated with theGammaproteobacteria(mainly potentially pathogenicStenotrophomonasstrains) and 50% with theBacilli, whereas all 96 isolates from rain-fed soils (48 from dry and 48 from rainy season soils) were affiliated with theBacilli. Up to six types of antibiotic resistance were found in isolates from wastewater-irrigated soils; sulfamethoxazole resistance was the most abundant (33.3% of the isolates), followed by oxacillin resistance (21.9% of the isolates). In summary, we detected an increase of potentially harmful bacteria and a larger incidence of resistance determinants in wastewater-irrigated soils, which might result in health risks for farm workers and consumers of wastewater-irrigated crops.

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Biochar and compost effects on soil microbial communities and nitrogen induced respiration in turfgrass soils

PLoS ONE ◽

10.1371/journal.pone.0242209 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242209

Author(s):

Muhammad Azeem ◽

Lauren Hale ◽

Jonathan Montgomery ◽

David Crowley ◽

Milton E. McGiffen

Keyword(s):

Microbial Community ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Community Structures ◽

Soil Microbial Community Structure ◽

Amended Soils ◽

Soil Microbial ◽

Compost Amendment ◽

Microbial Community Structures

We examined the effect of a labile soil amendment, compost, and recalcitrant biochar on soil microbial community structure, diversity, and activity during turfgrass establishment. Two application rates of biochar (B1 at 12.5 t ha-1and B2 at 25 t ha-1), a 5 centimeter (cm) green waste compost treatment (CM) in top soil, a treatment with 12.5 t ha-1 biochar and 5 cm compost (B1+CM), and an unamended control (CK) treatment were prepared and seeded with tall fescue. Overall, results of phospholipid fatty acid analysis (PLFA) profiling and Illumina high-throughput sequencing of 16S rRNA genes amplified from soil DNA revealed significant shifts in microbial community structures in the compost amended soils whereas in biochar amended soils communities were more similar to the control, unamended soil. Similarly, increases in enzymatic rates (6–56%) and nitrogen-induced respiration (94%) were all largest in compost amended soils, with biochar amended soils exhibiting similar patterns to the control soils. Both biochar and compost amendments impacted microbial community structures and functions, but compost amendment, whether applied alone or co-applied with biochar, exhibited the strongest shifts in the microbial community metrics examined. Our results suggest application of compost to soils in need of microbiome change (reclamation projects) or biochar when the microbiome is functioning and long-term goals such as carbon sequestration are more desirable.

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Investigation of Sources, Diversity, and Variability of Bacterial Aerosols in Athens, Greece: A Pilot Study

Atmosphere ◽

10.3390/atmos13010045 ◽

2021 ◽

Vol 13 (1) ◽

pp. 45

Author(s):

Angelina Metaxatos ◽

Sydonia Manibusan ◽

Gediminas Mainelis

Keyword(s):

Field Application ◽

16S Rrna Genes ◽

Rrna Genes ◽

Airborne Bacteria ◽

Urban Air ◽

Operational Taxonomic Units ◽

Bacterial Aerosol ◽

Bacterial Aerosols ◽

Taxonomic Categories

We characterized the composition, diversity, and potential bacterial aerosol sources in Athens’ urban air by DNA barcoding (analysis of 16S rRNA genes) during three seasons in 2019. Air samples were collected using the recently developed Rutgers Electrostatic Passive Sampler (REPS). It is the first field application of REPS to study bacterial aerosol diversity. REPS samplers captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, we detected 793 operational taxonomic units (OTUs), which were fully classified into the six distinct taxonomic categories (Phylum, Class, Order, etc.). These OTUs belonged to Phyla Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. We found a complex community of bacterial aerosols with several opportunistic or potential pathogens in Athens’ urban air. Referring to the available literature, we discuss the likely sources of observed airborne bacteria, including soil, plants, animals, and humans. Our results on bacterial diversity are comparable to earlier studies, even though the sampling sites are different or geographically distant. However, the exact functional and ecological role of bioaerosols and, even more importantly, their impact on public health and the ecosystem requires further air monitoring and analysis.

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Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab007 ◽

2021 ◽

Author(s):

Gabriela Fernandez-Gnecco ◽

Kornelia Smalla ◽

Lorrie Maccario ◽

Søren J Sørensen ◽

Pablo Barbieri ◽

...

Keyword(s):

Microbial Community ◽

Cover Crops ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Temporal Shift ◽

Soil Microbial ◽

No Till

Abstract Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.

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Gas Exchange during Lung Perfusion/Ventilation during Cardiopulmonary Bypass: Preliminary Results of a Pilot Study

Open Journal of Cardiovascular Surgery ◽

10.4137/ojcs.s4109 ◽

2010 ◽

Vol 3 ◽

pp. OJCS.S4109 ◽

Cited By ~ 3

Author(s):

Francisco Igor B. Macedo ◽

Enisa M. Carvalho ◽

Edward Gologorsky ◽

Michael Barron ◽

Mohammed Hassan ◽

...

Keyword(s):

Cardiopulmonary Bypass ◽

Pilot Study ◽

Gas Exchange ◽

Ischemic Injury ◽

Lung Perfusion ◽

Preliminary Results

Lung perfusion/ventilation was introduced as a means to minimize cardiopulmonary (CPB)-related pulmonary ischemic injury. Current results in the literature are divergent, and the role of gas exchange during lung perfusion/ventilation during CPB, remains undefined. This report details a) the technique of continuous lung perfusion/ventilation during CPB, b) provides initial observations, and c) discusses gas exchange during CPB.

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Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages

BMC Microbiology ◽

10.1186/s12866-020-02081-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ai-Zi Tong ◽

Wei Liu ◽

Qiang Liu ◽

Guang-Qing Xia ◽

Jun-Yi Zhu

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Panax Ginseng ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Continuous Cropping ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Soil Borne Pathogens

Abstract Background Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored. Methods Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity. Results The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng. Conclusion Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community.

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