Soil bacterial community mediates the effect of labile carbon on methanogenic decomposition of soil organic matter

Input of plant material may strongly change decomposition rates of soil organic matter (SOM), i.e. causing priming effect (PE), but the underlying mechanisms are largely unknown. We found that rice straw addition in anoxic Fuyang (F) rice field soil stimulated CH4 production from SOM at the expense of CO2, whereas in Uruguay (U) soil it suppressed SOM degradation to CO2 plus CH4 (negative PE). Reciprocal inoculation experiments with non-sterile and sterile soils showed that the soils always displayed the effect of rice straw characteristic for the live microbial community rather than for the soil physicochemical properties. Pyrosequencing of 16S rRNA genes showed that bacterial communities in these soil samples were separated into two clusters (F and U). Symbiobacterium was abundant or dominant in microbiota from U soil, but negligible in those from F soil. Network analysis indicated that the bacterial populations involved in SOM decomposition were different between soils of F and U clusters; moreover, they were more tightly connected to methanogens in U than in F clusters. Ultimately, our results suggested that the PE of rice straw is mediated by the composition and activity of soil microbial community

Structure and function of methanogenic microbial communities in soils from flooded rice and upland soybean fields from Sanjiang plain, NE China.

About 50 years ago, most of the natural wetlands in northeast China, the Sanjiang plain, were converted to either flooded rice fields or to upland soybean fields. After the conversion, natural wetland soils were either managed as artificial wetland or as drained upland resulting in soil microbial community changes. The purpose of our study was to understand how methanogenic microbial communities and their functions had changed in the two different soils upon conversion, and whether these communities now exhibit different resistance/resilience to drying and rewetting. Therefore, we determined function, abundance and composition of the methanogenic archaeal and bacterial communities in two soils reclaimed from a Carex wetland 25 years ago. We incubated the soils under anoxic conditions and measured the rates and pathways of CH4 production by analyzing concentration and ?13C of CH4 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also analyzed the abundance of bacterial and archaeal 16S rRNA genes, and of mcrA (coding for a subunit of the methyl coenzyme M reductase) using qPCR. The composition of the archaeal and bacterial 16S rRNA genes was determined by using MiSeq illumina sequencing. Our results showed clear differences in structure and function of methanogenic archaeal communities in rice field soil versus upland soil. Furthermore, in both soils composition of bacteria and archaea changed after artificial drying and became less diverse. The archaeal and bacterial signature species in the two soils were also different. However, functional changes were similar, with rates of CH4 production and contribution of aceticlastic methanogenesis decreasing upon drying and rewetting in both soils

Response of methanogenic microbial communities to desiccation stress in flooded and rain-fed paddy soil from Thailand

Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ13C of organic carbon and of CH4 and CO2 produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR) of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase) and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH4 production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity). The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased

Isolation of nitrogen-fixing endophytic bacteria in rice plants grown in different soils

El arroz (Oryza sativa) es uno de los principales rubros de exportación agrícola de Uruguay. Es imprescindible encontrar nuevas herramientas que potencien el desempeño del cultivo y mejoren la utilización de nutrientes con un adecuado margen de seguridad alimentaria y ambiental. Las bacterias endófitas son aquellas que se desarrollan en tejidos internos de la planta sin causar síntomas de daño en ella. Pueden tener un impacto importante en la productividad de cereales estimulando el crecimiento de la planta por mecanismos como la producción de hormonas, el antagonismo de patógenos o la fijación de nitrógeno atmosférico (diazótrofas). El uso de inoculantes biológicos en lugar de fertilizantes químicos nitrogenados es una estrategia que disminuye el impacto ambiental causado por los agroquímicos. El objetivo de este trabajo es aislar bacterias endófitas diazótrofas en plantas de arroz sembradas en distintos suelos con y sin historia de cultivo. El ensayo se realizó en fitotrón sembrando semillas esterilizadas superficialmente en suelos de diferente origen y características. Se evaluó el rendimiento vegetal a los 20 días incubación. Se aislaron bacterias diazótrofas de raíz y de parte aérea cultivadas en diferentes medios variando las condiciones de incubación para recuperar diazótrofos aerobios, anaerobios esporulados y fotótrofos.Rice (Oryza sativa) is a major agricultural product exported by Uruguay. It is imperative to find new tools to increase the yield and to improve the crop nutrient utilization keeping sustainable and healthy conditions of production. Endophytic bacteria grow in internal vegetal tissues without causing symptoms of damage to the plant. They can have a major impact on the cereal productivity by stimulating plant growth by mechanisms such as hormone production, antagonism of pathogens or atmospheric nitrogen fixation (diazotrophic bacteria). The use of biological inoculants instead of chemical nitrogen fertilizers is a strategy that reduces the environmental impact of agrochemicals. The objective of this work is to isolate endophytic diazotrophyc bacteria in rice planted in different soils from Uruguay. The assay was performed in controlled conditions sowing sterilized seeds in soils of different origin and characteristics. Plants yield was evaluated after 20 days of incubation. Diazotrophic bacteria were isolated from roots and aerial tissues of the plants. Different culture media and incubation conditions were used to recover aerobic, anaerobic sporulated and anoxigenic phototrophic bacteria. More than 50 isolates were obtained and tested for the diazotrophic activity and for the amplification of nifH gene. The diversity of the isolates was analyzed by ARDRA (Amplified Ribosomal DNA Restriction Analysis). The identification was performed by 16S rRNA gene sequencing. The main species detected were Azospirillum lipoferum, Herbaspirillum seropedicae, Enterobacter cloacae and Paenibacillus graminis. These strains could be good tools to develop inoculants to promote the growth in rice plants.Asociación de Universidades Grupo Montevide

Selection and characterization of bacterial consortium as a tool for bioremediation of atrazine contamination in water treatment plants

El uso expandido a nivel mundial, la persistencia y toxicidad del herbicida atrazina y sus metabolitos llevaron a que se conviertan en uno de los contaminantes más comunes en aguas superficiales y subterráneas, excediendo en algunos casos los límites máximos permitidos por la EPA de 3 ppb. A pesar que la atrazina puede ser degradada abióticamente, la biológica es la vía de degradación más importante a pH neutro y es la única que podría terminar en CO2 y NH4. La degradación biológica de la atrazina que puede llevarse a cabo por especies de bacterias aisladas como Pseudomonas sp. strain ADP o por consorcios de bacterias relativamente sencillos que fueron obtenidos de suelos con una historia larga de contaminación. En este estudio, el foco se centró en obtener consorcios de bacterias capaces de degradar atrazina en muestras tomadas del agua que ingresa a diferentes plantas potabilizadoras (Aguas Corrientes, Dolores y Florida) que estuvieron esporádicamente expuestos a pulsos de atrazina en bajas concentraciones. Se realizaron ensayos en microcosmos con atrazina a una concentración de 20 ppm con o sin el agregado de otra fuente de nitrógeno (NO3 -) y dos temperaturas de incubación diferentes (20°C y 30°C). La estabilidad del los consorcios se probó mediante repiques sucesivos en un medio mínimo (MDA) manteniendo las mismas condiciones previas. En todos los casos la degradación de atrazina se midió por UV-HPLC. Adicionalmente, se amplificaron por PCR los genes de la vía metabólica de degradación de la atrazina atzA, trzN, atzB, atzC, atzD and trzD para confirmar su presencia en los. Cuatro de doce tratamientos en el ensayo en microcosmos degradaron atrazina en un período de 11 días en Aguas Corrientes y Dolores. Las muestras de Florida no mostraron degradación de atrazina.The worldwide use, persistence, and toxicity of the herbicide atrazine and its metabolites have led to them becoming a common contaminant in surface and ground water at levels that sometimes exceed the maximum allowed by the US-EPA of 3 ppb. Although atrazine can be degraded abiotically, the biological is the most important at neutral pH and is the unique way that could degrade atrazine completely to NH4 and CO2. Atrazine biodegradation has previously been shown to be carried out by several individual bacterial species such as Pseudomonas sp. strain ADP or by relatively simple bacterial consortia that have been enriched from large history contaminated soils. This study was focused on obtaining stable microbial consortium capable of degrade atrazine taken from incoming water of different potabilization treatment plants from Uruguay (Aguas Corrientes, Dolores y Florida) that have sporadically been exposure to low pulses of atrazine. We prepared microcosms assays with atrazine at a concentration of 20 ppm with or without other inorganic nitrogen amendment (NO3 -) and two different incubation temperatures (20 °C and 30 °C). Stability of the bacterial consortium was tested by successive enrichment in an atrazine minimal medium (MDA) maintaining the same previous conditions. In all cases, atrazine degradation was monitored by UVHPLC. In addition, atrazine metabolic genes atzA, trzN, atzB, atzC, atzD and trzD were amplified by PCR to confirm genetic stability. Four of the twelve microcosms assays showed atrazine degradation in a period of 11 days at different incubation conditions from samples from Dolores and Aguas Corrientes. Florida did not show atrazine degradation activity.Asociación de Universidades Grupo Montevide