scholarly journals Archaeal and methanogenic communities in the rice field under different fertilizer applications

2019 ◽  
Vol 20 (12) ◽  
Author(s):  
Yuli Fatma ◽  
IMAN RUSMANA ◽  
ARIS TRI WAHYUDI ◽  
HAMIM
Keyword(s):  
Rice Field ◽  
Methanogenic Archaea ◽  
Archaeal Community ◽  
Amplicon Sequencing ◽  
Fertilizer Application ◽  
Emission Rates ◽  
Ch4 Emission ◽  
Dominant Group ◽  
Methanogenic Community ◽  
Growing Period

Abstract. Fatma YS, Rusmana I, Wahyudi AT, Hamim. 2019. Archaeal and methanogenic communities in the rice field under different fertilizer applications. Biodiversitas 20: 3667-3675. The archaeal community in the soil surrounding rice roots plays key roles in biogeochemical cycles. Methanogenic archaea contribute to CH4 production in the rice field and control CH4 emission rates; an important greenhouse gas significantly emitted from the rice field. Characteristic of archaeal and methanogenic community in Indonesian rice field has not been well documented. In this study, rice plants grown in the rice field were treated with two different fertilizer applications, i.e., 100% urea without biofertilizer (250 kg ha-1) (B0), and 50% urea (125 kg ha-1) with biofertilizer consisted of methanotrophic bacteria and N2O-reducing bacteria (B1). Soil archaeal community of the two types of fertilization was characterized over the rice-growing period using 16S rRNA amplicon sequencing. The succession and dynamic of the archaeal population were detected in each of the two treatments before fertilizer application (0 days after transplanting [DAT]) until the rice generative phase (69 DAT). During the period, the archaeal soil community in both treatments was dominated by Crenarchaeota. The relative abundance of putative methanogens was higher in the B0 treatment than that of B1 treatment. Within the methanogenic community, Methanosarcinaceae and Methanomassiliicoccaceae which found as most dominant group in both treatments were presumably to be important contributors to CH4 emission. The application of 50% urea with biofertilizer (B1) changed the structure of the archaeal and methanogenic community in the rice field compared to the application of 100% urea (B0).

Beyond the usual suspects: methanogenic communities in eastern North American peatlands are also influenced by nickel and copper concentrations

2021 ◽  
Author(s):  
Sydney E Bear ◽  
James D Seward ◽  
Louis Jamie Lamit ◽  
Nathan Basiliko ◽  
Tim Moore ◽  
...  
Keyword(s):  
Strong Predictor ◽  
Methanogenic Archaea ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Contaminated Sites ◽  
Methanogenic Community ◽  
Primary Driver ◽  
High Concentrations ◽  
Methyl Coenzyme M Reductase ◽  
Eastern Half

Abstract Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analyzed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.

Isolasi dan Karakterisasi Bakteri Tanah Sawah di Kecamatan Medan Satria dan Bekasi Utara, Kota Bekasi, Jawa Barat

2017 ◽  
Vol 3 (4) ◽  
pp. 187 ◽  
Author(s):  
Arief Pambudi ◽  
Nita Noriko ◽  
Endah Permata Sari
Keyword(s):  
Plant Growth ◽  
Soil Bacteria ◽  
Rice Field ◽  
Plant Growth Promoting Rhizobacteria ◽  
Fertilizer Application ◽  
Rice Production ◽  
Production Costs ◽  
Soil Conditions ◽  
Nitrogen Fixation Activity ◽  
Growth Promoting

<p><em>Abstrak -</em><strong> </strong><strong>Produksi padi di Indonesia setiap tahun mengalami peningkatan, namun peningkatan ini belum mampu memenuhi kebutuhan nasional sehingga impor masih harus dilakukan. Salah satu masalah dalam produksi beras adalah penggunaan pupuk berlebih yang tidak hanya meningkatkan biaya produksi, namun juga merusak kondisi tanah. Aplikasi bakteri tanah sebagai Plant <em>Growth Promoting Rhizobacteria</em> (PGPR) dapat menjadi salah satu solusi terhadap masalah ini. Penelitian ini bertujuan untuk mengisolasi bakteri tanah dari 3 lokasi sawah daerah Bekasi, membandingkan keberadaan total bakteri pada ketiga lokasi tersebut,  dan melakukan karakterisasi isolat berdasarkan karakter yang dapat memicu pertumbuhan tanaman. Dari ketiga lokasi, diperoleh total 59 isolat dan 5 diantaranya berpotensi sebagai PGPR karena kemampuan fiksasi Nitrogen, melarutkan Fosfat, katalase positif, dan motil. Dari ketiga lokasi pengambilan sampel, BK1 memiliki jumlah total bakteri terendah karena aplikasi pemupukan dan pestisida berlebih yang ditandai tingginya kadar P total, serta tingginya residu klorpirifos, karbofuran, dan paration. Kondisi fisik tanah BK1 juga didominasi partikel liat yang menyebabkan tanah menjadi lebih padat. Peningkatan jumlah penggunaan pupuk tidak selalu diikuti peningkatan produktivitas tanaman.</strong></p><p> </p><p><strong><em>Kata Kunci</em></strong><strong><em> </em></strong>- <em>Bakteri tanah, Rhizosfer sawah, PGPR, Pupuk Hayati</em></p><p><strong> </strong></p><p><em>Abstract</em><strong> - </strong><strong>Rice production in Indonesia has increased annually, but this increase has not reached national demand,so imports still done. </strong><strong>One of the problems in rice production is the use of excessive fertilizers that not only increase production costs, but also decreased the soil conditions. The application of soil bacteria as Plant Growth Promoting Rhizobacteria (PGPR) can be the one solution to face this problem. The objective of this study was isolate soil bacteria from 3 locations of rice field in Bekasi, compare the total bacteria in the three locations, and characterize isolates based on the character that can promote plant growth. From three locations, a total of 59 isolates were obtained and 5 of them were potential as a PGPRs due to its Nitrogen fixation activity, Phosphate solubilization, positive catalase, and motility. From three sampling sites, BK1 has the lowest TPC value because of excessive  fertilizers and pesticides application which indicated by high total P levels, and also high chlorpyrifos, carbofuran and paration residues. The physical condition of BK1 soil is also dominated by clay particles which causes the soil more solid. Increasing of fertilizer application is not always followed by increased plant productivity.</strong></p><p><strong> </strong></p><p><strong><em>Keywords</em></strong> - <em>Biofertilizer, PGPR, Rice field rhizosphere, Soil Bacteria</em></p>

scholarly journals Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Yendi E. Navarro-Noya ◽  
César Valenzuela-Encinas ◽  
Alonso Sandoval-Yuriar ◽  
Norma G. Jiménez-Bueno ◽  
Rodolfo Marsch ◽  
...  
Keyword(s):  
Species Richness ◽  
Alpha Diversity ◽  
Methanogenic Archaea ◽  
Archaeal Community ◽  
Soil Samples ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Phylogenetic Information ◽  
Archaeal Communities ◽  
Saline Alkaline Soils

In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic CandidatusNitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils.Halobiforma,Halostagnicola,Haloterrigena, andNatronomonaswere found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.

scholarly journals Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

Archaea ◽  
2005 ◽  
Vol 1 (6) ◽  
pp. 391-397 ◽  
Author(s):  
Atsuo Sugano ◽  
Hidetaka Tsuchimoto ◽  
Tun Cho Cho ◽  
Makoto Kimura ◽  
Susumu Asakawa
Keyword(s):  
Rice Straw ◽  
Rice Field ◽  
Previous History ◽  
Methanogenic Archaea ◽  
Leaf Sheath ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Crop Season ◽  
Rdna Sequencing ◽  
Archaeal Communities

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related toMethanomicrobialesand Rice cluster I.Methanomicrobiales, Rice cluster I andMethanosarcinaleswere major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related toMethanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.

Composition of the archaeal community involved in methane production during the decomposition of Microcystis blooms in the laboratory

2012 ◽  
Vol 58 (10) ◽  
pp. 1153-1158 ◽  
Author(s):  
Peng Xing ◽  
Huabing Li ◽  
Qing Liu ◽  
Jiuwen Zheng
Keyword(s):  
Lake Taihu ◽  
Archaeal Community ◽  
Oxygen Depletion ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Methanogenic Community ◽  
Controlled Systems ◽  
Microcystis Blooms ◽  
Different Temperatures

We investigated the microbial processes involved in methane (CH4) production from Microcystis bloom scums at different temperatures. A Microcystis slurry was collected from Lake Taihu and incubated in airtight bottles at 15, 25, and 35 °C. The production of CH4 was monitored, and the emission rate was calculated. The dynamics of the methanogenic community were analyzed by terminal restriction fragment length polymorphism analysis of archaeal 16S rRNA genes. Phylogenetic information for the methanogens was obtained by cloning and sequencing selected samples. Significant CH4 emission from the Microcystis scums was delayed by approximately 12 days by the natural oxygen depletion process, and CH4 production was enhanced at higher temperatures. Phylogenetic analysis indicated that the archaeal community was composed of Methanomicrobiales, Methanobacteriaceae, and a novel cluster of Archaea. An apparent succession of the methanogenic community was demonstrated, with a predominance of Methanobacteriaceae at higher temperatures. Higher temperatures enhanced the methanogenic transformation of the Microcystis biomass and the phylogenetic dominance of hydrogenotrophic methanogens, suggesting that H2 and CO2 might be the primary substrates for CH4 production during Microcystis decomposition without the participation of lake sediment. This work provides insight into the microbial components involved in Microcystis biomass fermentation in controlled systems.

A comment on scaling methane emissions from vegetation and grazing ruminants in New Zealand

2006 ◽  
Vol 33 (7) ◽  
pp. 613 ◽  
Author(s):  
Francis M. Kelliher ◽  
Harry Clark ◽  
Zheng Li ◽  
Paul C. D. Newton ◽  
Anthony J. Parsons ◽  
...  
Keyword(s):  
New Zealand ◽  
Standard Deviation ◽  
Forest Canopy ◽  
Emission Rate ◽  
Oxidative Capacity ◽  
Emission Rates ◽  
Ch4 Emission ◽  
Ch4 Emissions ◽  
Grazed Pasture ◽  
Indigenous Forest

Keppler et al. (2006, Nature 439, 187–191) showed that plants produce methane (CH4) in aerobic environments, leading Lowe (2006, Nature 439, 148–149) to postulate that in countries such as New Zealand, where grazed pastures have replaced forests, the forests could have produced as much CH4 as the ruminants currently grazing these areas. Estimating CH4 emissions from up to 85 million ruminants in New Zealand is challenging and, for completeness, the capacity of forest and pastoral soils to oxidise CH4 should be included. On average, the CH4 emission rate of grazing ruminants is estimated to be 9.6 ± 2.6 g m–2 year–1 (±standard deviation), six times the corresponding estimate for an indigenous forest canopy (1.6 ± 1.1 g m–2 year–1). The forest’s soil is estimated to oxidise 0.9 ± 0.2 g m–2 year–1 more CH4 than representative soils beneath grazed pasture. Taking into account plant and animal sources and the soil’s oxidative capacity, the net CH4 emission rates of forest and grazed ecosystems are 0.6 ± 1.1 and 9.8 ± 2.6 g m–2 year–1, respectively.

scholarly journals The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

2015 ◽  
Vol 12 (21) ◽  
pp. 18103-18150 ◽  
Author(s):  
L. Purkamo ◽  
M. Bomberg ◽  
R. Kietäväinen ◽  
H. Salavirta ◽  
M. Nyyssönen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Keystone Species ◽  
Carbon Assimilation ◽  
Sugar Metabolism ◽  
Archaeal Community ◽  
Amino Sugar ◽  
Amplicon Sequencing ◽  
Fracture Zones ◽  
Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

scholarly journals Measuring N2O Emissions from Multiple Sources Using a Backward Lagrangian Stochastic Model

Atmosphere ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1277
Author(s):  
Cheng-Hsien Lin ◽  
Richard H. Grant ◽  
Cliff T. Johnston
Keyword(s):  
Management Practices ◽  
Cropping System ◽  
Fertilizer Application ◽  
N2o Emission ◽  
N2o Emissions ◽  
Emission Rates ◽  
Multiple Sources ◽  
Maize Production ◽  
Emissions Modeling ◽  
Short Period

Nitrous oxide (N2O) emissions from agricultural soil are substantially influenced by nitrogen (N) and field management practices. While routinely soil chambers have been used to measure emissions from small plots, measuring field-scale emissions with micrometeorological methods has been limited. This study implemented a backward Lagrangian stochastic (bLS) technique to simultaneously and near-continuously measure N2O emissions from four adjacent fields of approximately 1 ha each. A scanning open-path Fourier-transform infrared spectrometer (OP-FTIR), edge-of-field gas sampling and measurement, locally measured turbulence, and bLS emissions modeling were integrated to measure N2O emissions from four adjacent fields of maize production using different management in 2015. The maize N management treatments consisted of 220 kg NH3-N ha−1 applied either as one application in the fall after harvest or spring before planting or split between fall after harvest and spring before planting. The field preparation treatments evaluated were no-till (NT) and chisel plow (ChP). This study showed that the OP-FTIR plus bLS method had a minimum detection limit (MDL) of ±1.2 µg m−2 s−1 (3σ) for multi-source flux measurements. The average N2O emission of the four treatments ranged from 0.1 to 2.3 µg m−2 s−1 over the study period of 01 May to 11 June after the spring fertilizer application. The management of the full-N rate applied in the fall led to higher N2O emissions than the split-N rates applied in the fall and spring. Based on the same N application, the ChP practice tended to increase N2O emissions compared with NT. Advection of N2O from adjacent fields influenced the estimated emissions; uncertainty (1σ) in emissions was 0.5 ± 0.3 µg m−2 s−1 if the field of interest received a clean measured upwind background air, but increased to 1.1 ± 0.5 µg m−2 s−1 if all upwind sources were advecting N2O over the field of interest. Moreover, higher short-period emission rates (e.g., half-hour) were observed in this study by a factor of 1.5~7 than other micrometeorological studies measuring N2O-N loss from the N-fertilized cereal cropping system. This increment was attributed to the increase in N fertilizer input and soil temperature during the measurement. We concluded that this method could make near-continuous “simultaneous” flux comparisons between treatments, but further studies are needed to address the discrepancies in the presented values with other comparable N2O flux studies.

scholarly journals Dynamics of the Methanogenic Archaea in Tropical Estuarine Sediments

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
María del Rocío Torres-Alvarado ◽  
Francisco José Fernández ◽  
Florina Ramírez Vives ◽  
Francisco Varona-Cordero
Keyword(s):  
Organic Carbon ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Coastal Lagoons ◽  
Spatial Dynamics ◽  
Methanogenic Archaea ◽  
Estuarine Sediments ◽  
Microbiological Analysis ◽  
Methanogenic Community ◽  
Solids Content

Methanogenesis may represent a key process in the terminal phases of anaerobic organic matter mineralization in sediments of coastal lagoons. The aim of the present work was to study the temporal and spatial dynamics of methanogenic archaea in sediments of tropical coastal lagoons and their relationship with environmental changes in order to determine how these influence methanogenic community. Sediment samples were collected during the dry (February, May, and early June) and rainy seasons (July, October, and November). Microbiological analysis included the quantification of viable methanogenic archaea (MA) with three substrates and the evaluation of kinetic activity from acetate in the presence and absence of sulfate. The environmental variables assessed were temperature, pH, Eh, salinity, sulfate, solids content, organic carbon, and carbohydrates. MA abundance was significantly higher in the rainy season (106–107 cells/g) compared with the dry season (104–106 cells/g), with methanol as an important substrate. At spatial level, MA were detected in the two layers analyzed, and no important variations were observed either in MA abundance or activity. Salinity, sulfate, solids, organic carbon, and Eh were the environmental variables related to methanogenic community. A conceptual model is proposed to explain the dynamics of the MA.

Feeding lucerne silage to beef cattle at three allowances and four feeding frequencies affects circadian patterns of methane emissions, but not emissions per unit of intake

2014 ◽  
Vol 54 (9) ◽  
pp. 1350 ◽  
Author(s):  
Arjan Jonker ◽  
German Molano ◽  
Christopher Antwi ◽  
Garry Waghorn
Keyword(s):  
Emission Rate ◽  
Circadian Variation ◽  
Emission Rates ◽  
Ch4 Emission ◽  
Feeding Frequency ◽  
Ch4 Emissions ◽  
Time To Peak ◽  
Ch4 Production ◽  
Ad Libitum ◽  
Circadian Patterns

The objective of this study was to determine the circadian variation in methane (CH4) emissions from cattle fed lucerne silage at different feeding levels and feeding frequencies, to assist with interpretation of short ‘snapshot’ CH4 measurements used for predicting daily emissions. Eight Hereford × Friesian heifers (initially 20 months of age) were used in five consecutive periods (P1–5) of 14 days with CH4 emissions measured using respiration chambers for two consecutive days at the end of each period. Feed was restricted to intakes of ~6, 8, 8, 8 and 11 ± 1.3 (ad libitum) kg lucerne silage dry matter (DM), fed in 2, 2, 3, 4 or ad libitum (refilled twice daily) meals per day in P1–5, respectively. Daily CH4 production (g/day) was lower in P1 than in P2–4 (P < 0.05), which were lower than in P5 (P < 0.05), but CH4 yield (24.3 ± 1.23 g/kg DM) was unaffected by treatment. Among the five periods, CH4 emission rate (g/h) before feeding ranged from 1.8 to 6.5 g/h, time to peak CH4 production after start of feeding ranged from 19 to 40 min and peak CH4 production rate ranged from 11.1 to 17.5 g/h. The range in hourly CH4 emission rates during the day decreased with increasing feed intake level, but was unaffected by feeding frequency. In summary, the circadian pattern of CH4 emissions was affected by feed allowance and feeding frequency, and variation in CH4 emission rate was reduced with increasing intake, without affecting average daily yield (g CH4/kg DM intake).

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