scholarly journals Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow

2019 ◽  
Author(s):  
Mohammad Ghashghavi ◽  
Eric R. Hester ◽  
Viktoria Oliver ◽  
Claudia Lüke ◽  
Mike S. M. Jetten ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Paddy Field ◽  
Amplicon Sequencing ◽  
Rice Production ◽  
Paddy Fields ◽  
Rrna Gene ◽  
Classical Source ◽  
The Difference ◽  
Productive Land ◽  
Source Sink

AbstractMethane is a potent greenhouse gas that contributes to global warming. However, under certain conditions, its release into the atmosphere can be mitigated by methane-oxidizing microorganisms. Typically, cultivated wetlands (i.e., paddy fields) are a major source of methane (CH4) while forests and meadow uplands are considered to be CH4 sinks. As the global need for rice production increases each year, more uplands are converted to inundated paddy fields. To investigate soils that may be converted into productive land for rice production, we investigated a paddy field and adjacent meadow in Northern Italy. Using a combination of 16S rRNA gene amplicon sequencing to analyze the bacterial community, and gas flux measurements to quantify CH4 emissions, we looked for differences between classically defined CH4 sinks (meadow soils) and CH4 sources (paddy fields). Analysis of the total bacterial community revealed that the family Fimbriimonadaceae, which belongs to the phylum Armatimonadetes, was significantly higher in paddy field soils driving the difference between paddy and meadow soils. Whereas, we found that the methylotrophic families Methyloligellaceae and Methylomirabilaceae were also present in higher relative abundance in the paddy field. Despite these major differences, CH4 fluxes were highly variable between the two sites with no significant differences observed. Furthermore, we found the Methylomonaceae family to be more abundant at the center of a neighboring paddy field compared to the edge of the paddy field from the current study, hinting at methanotrophic variation based on location. Taking these results into account, we propose a conceptual model to explain possible scenarios that may result in paddy and meadow fields not exhibiting classical source/sink properties. These findings call for caution when including paddy and meadow areas separately into global CH4 flux calculations, and urge further research to discern drivers of CH4 cycling under a range of environmental conditions rather than relying on assumptions.

scholarly journals The Value of a Decrease in Temperature by One Degree Celsius of the Regional Microclimate—The Cooling Effect of the Paddy Field

Atmosphere ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 353
Author(s):  
Ya-Wen Chiueh ◽  
Chih-Hung Tan ◽  
Hsiang-Yi Hsu
Keyword(s):  
Land Use ◽  
Surface Temperature ◽  
Paddy Field ◽  
Research Area ◽  
Paddy Fields ◽  
Cooling Effect ◽  
Field Temperature ◽  
Bare Land ◽  
The Face ◽  
The Difference

In the face of climate change, extreme climates are becoming more frequent. There were severe droughts in Taiwan in 2020, 2014–2015, and 2002. In these years, the paddy fields were kept fallow to save water and transfer agricultural water to non-agricultural use. On the other hand, with global warming, the existence of paddy fields may be one of the natural solutions to regional temperature mitigation. This study used remote sensing to quantify the difference in temperature between paddy fields and urban areas. The result of overall surface temperature deductive analysis revealed that the temperature in the whole Taoyuan research area was 1.2 °C higher in 2002 than in 2003 because of fallowing of the paddy field, while in the Hsinchu research area, it was 1.5 °C higher in 2002 than in 2003, due to the same reason described above. In terms of the difference in land use, for the Hsinchu research area, the surface temperature deductive result showed that the average paddy field temperature in 2002 was 22.3 °C (sample area average), which was 7.7 °C lower than that of the building and road point and 4.3 °C lower than that of the bare land point. The average paddy field temperature in 2003 was 19.2 °C (sample area average), which was 10.1 °C lower than that of the building and road point and 8.3 °C lower than that of the bare land point. Then this study evaluated the economic valuation of the paddy field cooling effect using the contingent valuation method. Through the paddy field cooling effect and in the face of worsening extreme global climate, the willingness to pay (WTP) of the respondents in Taiwan for a decrease of 1 °C with regard to the regional microclimate was evaluated. It was found that people in Taiwan are willing to pay an extra 8.89 USD/per kg rice/year for the paddy for a decrease in temperature by 1 °C in the regional microclimate due to the paddy field. Furthermore, this study applied the benefits transfer method to evaluate the value of a decrease of 1 °C in the regional microclimate in Taiwan. The value of a decrease of 1 °C in the regional microclimate in Taiwan is 9,693,144,279 USD/year. In this regard, the economic value of 1 °C must not be underestimated. In conclusion, more caution is needed while making decisions to change the land use of paddy fields to other land uses.

Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

2019 ◽  
Author(s):  
Lara Parata ◽  
Shaun Nielsen ◽  
Xing Xing ◽  
Torsten Thomas ◽  
Suhelen Egan ◽  
...  
Keyword(s):  
Coral Reef ◽  
Gastrointestinal Tract ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Food Source ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Symbionts ◽  
Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

scholarly journals A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Jianxiao Song ◽  
Uli Klümper ◽  
Leise Riber ◽  
Arnaud Dechesne ◽  
Barth F Smets ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Amplicon Sequencing ◽  
Plasmid Transfer ◽  
Rrna Gene ◽  
Long Term Effects ◽  
Cu Contamination ◽  
Soil Bacterial

ABSTRACT Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg−1) soil compared to corresponding communities extracted from moderately (458 mg kg−1) Cu contaminated soil and a low Cu reference soil (15 mg kg−1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.

scholarly journals A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Siwen Deng ◽  
Heidi M.-L. Wipf ◽  
Grady Pierroz ◽  
Ted K. Raab ◽  
Rajnish Khanna ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Amendment ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Microbiome ◽  
Plant Growth Promoting ◽  
Miseq Platform ◽  
Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

A Rethink on the Origine of Songgungni Culture

2019 ◽  
pp. 91-125
Author(s):  
Jaeho Ahn
Keyword(s):  
Bronze Age ◽  
Paddy Field ◽  
Family System ◽  
Early Stage ◽  
Paddy Fields ◽  
Shandong Peninsula ◽  
Surplus Production ◽  
Ceramic Art ◽  
Burial Mounds ◽  
The Difference

Songgungni Culture, formed in the late Bronze Age of Korean peninsula, is characterized by the increased power of chieftains, uses of bronzeware, and constructions of huge burial mounds known as Guhoekmyo. The discussion on the difference of Songgungni Culture from previous cultural forms has been divided into the view to see it as foreign influences and that to see it derived from the previous local cultures. The author suggested the latter view first in 1992 but the findings accumulated since then lead us to rethink the origin of Songgungni Culture from a perspective that conjoins these two oft-conflicting views. The Zhou Dynasty and paddy field agrarian culture in the lower area of the Yangtze River influenced the formation of Songgungni Culture given the following findings. First, the Zhou Dynasty’s ceramic art called Beating Technique was discovered in Songgungni Culture with other artifacts such as weights made of stone, bottom parts of Chinese earthenware, and the jar coffins indicating the existence of ascribed status. Second, the excavations of paddy fields, Yunnan- style kilns, independent pillar structures, flask-shaped storage holes, and pestles suggest the propagation of the paddy field rice culture of the lower Yangtze along the coastline of the Shandong Peninsula. Under these foreign influences, Songguk-ri type potteries and other creative agricultural tools were produced. The differentiation of the previous joint family system into the nuclear produced lots of downsized dwelling areas which characterize Songguk-ri culture. And the innovation in the yielding capacity made possible by paddy fields also shows an aspect of Chiefdom settled into this area during the time. The surplus production of this period was not enough to advance towards the autonomous production of bronzeware. The increased size of chieftains’ tombs did not contain enough burial goods. Given the aforementioned findings, Songgungni Culture could be understood as an early stage of Chiefdom, just getting out of the state of fragmented society.

scholarly journals Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e41606 ◽  
Author(s):  
Sebastian Jünemann ◽  
Karola Prior ◽  
Rafael Szczepanowski ◽  
Inga Harks ◽  
Benjamin Ehmke ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Ion Torrent ◽  
Community Shift

scholarly journals Bacterial community shift in nutrient-treated oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery

2018 ◽  
Author(s):  
Thanachai Phetcharat ◽  
Pinan Dawkrajai ◽  
Thararat Chitov ◽  
Pisanu Wongpornchai ◽  
Schradh Saenton ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Microbial Enhanced Oil Recovery ◽  
Nutrient Treatment ◽  
Chemical Structures

AbstractMicrobial Enhanced Oil Recovery (MEOR) is a promising strategy to improve recovery of residual oil in reservoirs, which can be performed by promoting specific indigenous microorganisms. In this study, bacterial communities and the effects of elemental nutrient treatment of oil-bearing sandstone cores originated from six oil wells of an onshore reservoir was determined by tagged 16S rRNA gene amplicon sequencing, using Ion Torrent Metagenomic Sequencing Analysis. A total number of sequences were taxonomically classified into 43 phyla, 320 families, and 584 genera, with the dominant bacterial populations being related to Deinococcus-Thermus, and Betaproteobacteria. The nutrient treatment resulted in markedly increase in the relative abundance of Gammaproteobacteria. Thermus, Acinetobacter, and Pseudomonas were the most abundant genera. To our knowledge, this is the first report on the effect of elemental nutrients on alteration of bacteria communities attached to the oil-bearing rock. It provides comprehensive data on bacterial, physical, and chemical structures within a reservoir and demonstrates how these parameters can be co-analyzed to serve as a basis for designing a MEOR process. It also provides a model of how a bacterial community in reservoirs’ strata can be altered by nutrient treatment to enhance the efficiency of MEOR applications.

scholarly journals Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hannah E. Pilch ◽  
Andrew J. Steinberger ◽  
Donald C. Sockett ◽  
Nicole Aulik ◽  
Garret Suen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Pathogenic Bacteria ◽  
Bacterial Community Composition ◽  
Dairy Farm ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Recycling System ◽  
Core Microbiota ◽  
Relative Abundances

Abstract Background Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing. Results Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons. Conclusions These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

Influence of sampling and DNA extraction on 16S rRNA gene amplicon sequencing - Comparison of the bacterial community between two food processing plants

LWT ◽  
2018 ◽  
Vol 90 ◽  
pp. 186-192 ◽  
Author(s):  
Anna Kristina Witte ◽  
Christine Leeb ◽  
Beate Pinior ◽  
Patrick Mester ◽  
Susanne Fister ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
Food Processing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Processing Plants

scholarly journals Most of the Dominant Members of Amphibian Skin Bacterial Communities Can Be Readily Cultured

2015 ◽  
Vol 81 (19) ◽  
pp. 6589-6600 ◽  
Author(s):  
Jenifer B. Walke ◽  
Matthew H. Becker ◽  
Myra C. Hughey ◽  
Meredith C. Swartwout ◽  
Roderick V. Jensen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Batrachochytrium Dendrobatidis ◽  
Amplicon Sequencing ◽  
Reference Database ◽  
Rrna Gene ◽  
Amphibian Skin ◽  
Amphibian Species ◽  
Content Type ◽  
Average Percentage ◽  
Culture Independent

ABSTRACTCurrently, it is estimated that only 0.001% to 15% of bacteria in any given system can be cultured by use of commonly used techniques and media, yet culturing is critically important for investigations of bacterial function. Despite this situation, few studies have attempted to link culture-dependent and culture-independent data for a single system to better understand which members of the microbial community are readily cultured. In amphibians, some cutaneous bacterial symbionts can inhibit establishment and growth of the fungal pathogenBatrachochytrium dendrobatidis, and thus there is great interest in using these symbionts as probiotics for the conservation of amphibians threatened byB. dendrobatidis. The present study examined the portion of the culture-independent bacterial community (based on Illumina amplicon sequencing of the 16S rRNA gene) that was cultured with R2A low-nutrient agar and whether the cultured bacteria represented rare or dominant members of the community in the following four amphibian species: bullfrogs (Lithobates catesbeianus), eastern newts (Notophthalmus viridescens), spring peepers (Pseudacris crucifer), and American toads (Anaxyrus americanus). To determine which percentage of the community was cultured, we clustered Illumina sequences at 97% similarity, using the culture sequences as a reference database. For each amphibian species, we cultured, on average, 0.59% to 1.12% of each individual's bacterial community. However, the average percentage of bacteria that were culturable for each amphibian species was higher, with averages ranging from 2.81% to 7.47%. Furthermore, most of the dominant operational taxonomic units (OTUs), families, and phyla were represented in our cultures. These results open up new research avenues for understanding the functional roles of these dominant bacteria in host health.

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