Identification of active denitrifiers by DNA-Stable Isotope Probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer

Groundwater reservoirs constitute important freshwater resources. However, these ecosystems are highly vulnerable to contamination and have to rely on the resident microbiota to attenuate the impact of this contamination. Nitrate is one of the main contaminants found in groundwater and denitrification is the main process that removes the compound. In this study, the response to nutrient load on indigenous microbial communities in groundwater from a low impacted aquifer in Uruguay was evaluated. Denitrification rates were measured in groundwater samples from three different sites with nitrate, acetate and pyrite amendments. Results showed that denitrification is feasible under in situ nitrate and electron donor concentrations, although the lack of readily available organic energy source would limit the attenuation of higher nitrate concentrations. DNA Stable-isotope probing (SIP), combined with amplicon sequencing of 16S rRNA, nirS and nirK genes, was used to identify the active denitrifiers. Members of the phylum Betaproteobacteria were the dominant denitrifiers in two of three sites, with different families being observed; members of the genus Vogesella (Neisseriaceae) were key denitrifiers at one site, while the genera Dechloromonas (Rhodocyclaceae) or Comamonas (Comamonadaceae) were the main denitrifiers detected at the other sites

Sustainable and Low Greenhouse Gas Emitting Rice Production in Latin America and the Caribbean: A Review on the Transition from Ideality to Reality.

The burgeoning demand for rice in Latin America and Caribbean (LAC) exceeds supply, resulting in a rice deficit. To overcome this challenge, rice production should be increased, albeit sustainably. However, since rice production is associated with increases in the atmospheric concentration of two greenhouse gases (GHGs), namely methane (CH4) and nitrous oxide (N2O), the challenge is on ensuring that production increases are not associated with an increase in GHG emissions and thus do not cause an increase in GHG emission intensities. Based on current understanding of drivers of CH4 and N2O production, we provide here insights on the potential climate change mitigation benefits of management and technological options (i.e., seeding, tillage, irrigation, residue management) pursued in the LAC region. Studies conducted in the LAC region show intermittent irrigation or alternate wetting and drying of rice fields to reduce CH4 emissions by 25–70% without increasing N2O emissions. Results on yield changes associated with intermittent irrigation remain inconclusive. Compared to conventional tillage, no-tillage and anticipated tillage (i.e., fall tillage) cause a 21% and 25% reduction in CH4 emissions, respectively. From existing literature, it was unambiguous that the mitigation potential of most management strategies pursued in the LAC region need to be quantified while acknowledging country-specific conditions. While breeding high yielding and low emitting rice varieties may represent the most promising and possibly sustainable approach for achieving GHG emission reductions without demanding major changes in on-farm management practices, this is rather idealistic. We contend that a more realistic approach for realizing low GHG emitting rice production systems is to focus on increasing rice yields, for obvious food security reasons, which, while not reducing absolute emissions, should translate to a reduction in GHG emission intensities. Moreover, there is need to explore creative ways of incentivizing the adoption of promising combinations of management and technological options

Caloramator proteoclasticus sp. nov., a new moderately thermophilic anaerobic proteolytic bacterium

A new moderately thermophilic proteolytic anaerobe, strain UT, was isolated from mesophilic granular methanogenic sludge. The cells were spore-forming, motile rods that were 0.4 pm wide and 2.4 to 4 pm long and stained gram negative. Electron micrographs of thin sections revealed the presence of an atypical gram-positive cell wall. Optimum growth occurred at 55°C and at pH values between 7.0 and 7.5, with a doubling time of 30 min. The DNA base ratio of guanine plus cytosine was 31 mol%. The bacterium fermented proteins mainly to acetate, hydrogen, formate, and branched-chain fatty acids. Several amino acids, including glutamate, aspartate, arginine, histidine, threonine, methionine, and branched-chain amino acids, were also utilized. Glutamate was degraded to acetate, formate, hydrogen, and alanine. In addition, the strain degraded carbohydrates, including glucose, fructose, mannose, cellobiose, and starch, to acetate, ethanol, formate, lactate, and hydrogen. The results of a 16s rRNA sequence analysis phylogenetically placed strain UT in the low-guanine-plus-cytosine-content subgroup of the gram-positive phylum. We propose to classify the described strain in the genus Caloramator as a new species, Caloramator proteoclasticus. The type strain of C. proteoclasticus, strain U, has been deposited in the Deutsche Sammlung von Mikroorganismen as strain DSM 10124. Many types of industrial wastewaters are treated successfully in methanogenic bioreactors (17,30,32). Anaerobic treatmen

Yield-scaled global warming potential of two irrigation management systems in a highly productive rice system

ABSTRACT Water management impacts both methane (CH4) and nitrous oxide (N2O) emissions from rice paddy fields. Although controlled irrigation is one of the most important tools for reducing CH4emission in rice production systems it can also increase N2O emissions and reduce crop yields. Over three years, CH4 and N2O emissions were measured in a rice field in Uruguay under two different irrigation management systems, using static closed chambers: conventional water management (continuous flooding after 30 days of emergence, CF30); and an alternative system (controlled deficit irrigation allowing for wetting and drying, AWDI). AWDI showed mean cumulative CH4 emission values of 98.4 kg CH4 ha−1, 55 % lower compared to CF30, while no differences in nitrous oxide emissions were observed between treatments ( p > 0.05). No yield differences between irrigation systems were observed in two of the rice seasons ( p > 0.05) while AWDI promoted yield reduction in one of the seasons ( p< 0.05). When rice yield and greenhouse gases (GHG) emissions were considered together, the AWDI irrigation system allowed for lower yield-scaled total global warming potential (GWP). Higher irrigation water productivity was achieved under AWDI in two of the three rice seasons. These findings suggest that AWDI could be an option for reducing GHG emissions and increasing irrigation water productivity. However, AWDI may compromise grain yield in certain years, reflecting the importance of the need for fine tuning of this irrigation strategy and an assessment of the overall tradeoff between relationships in order to promote its adoption by farmers

Yield-scaled global warming potential of two irrigation management systems in a highly productive rice system

Water management impacts both methane (CH4) and nitrous oxide (N2O) emissions from rice paddy fields. Although controlled irrigation is one of the most important tools for reducing CH4emission in rice production systems it can also increase N2O emissions and reduce crop yields. Over three years, CH4 and N2O emissions were measured in a rice field in Uruguay under two different irrigation management systems, using static closed chambers: conventional water management (continuous flooding after 30 days of emergence, CF30); and an alternative system (controlled deficit irrigation allowing for wetting and drying, AWDI). AWDI showed mean cumulative CH4 emission values of 98.4 kg CH4 ha−1, 55 % lower compared to CF30, while no differences in nitrous oxide emissions were observed between treatments ( p >; 0.05). No yield differences between irrigation systems were observed in two of the rice seasons ( p >; 0.05) while AWDI promoted yield reduction in one of the seasons ( p< 0.05). When rice yield and greenhouse gases (GHG) emissions were considered together, the AWDI irrigation system allowed for lower yield-scaled total global warming potential (GWP). Higher irrigation water productivity was achieved under AWDI in two of the three rice seasons. These findings suggest that AWDI could be an option for reducing GHG emissions and increasing irrigation water productivity. However, AWDI may compromise grain yield in certain years, reflecting the importance of the need for fine tuning of this irrigation strategy and an assessment of the overall tradeoff between relationships in order to promote its adoption by farmers