Succession and community composition of ammonia-oxidizing archaea and bacteria in bulk soil of a Japanese paddy field

ABSTRACT Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase α-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.

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Soil properties have more significant effects on the community composition of protists than the rhizosphere effect of rice plants in alkaline paddy field soils

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2021.108397 ◽

2021 ◽

pp. 108397

Author(s):

Rasit ASILOGLU ◽

Keiko SHIROISHI ◽

Kazuki SUZUKI ◽

Oguz Can TURGAY ◽

Naoki HARADA

Keyword(s):

Soil Properties ◽

Community Composition ◽

Paddy Field ◽

Rhizosphere Effect ◽

Rice Plants ◽

Field Soils

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Effects of Different Land-use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils

Applied and Environmental Microbiology ◽

10.1128/aem.00092-21 ◽

2021 ◽

Author(s):

Xinli Wang ◽

Yun Wang ◽

Fei Zhu ◽

Chi Zhang ◽

Peiyao Wang ◽

...

Keyword(s):

Land Use ◽

Forest Soil ◽

Community Composition ◽

Organic Matter Content ◽

Soil Dna ◽

Ammonia Oxidizing Archaea ◽

Vegetable Soil ◽

Land Use Types ◽

Nitrite Oxidizing Bacteria ◽

Greenhouse Vegetable

Land-use types with different disturbance gradients show many variations in soil properties, but the effects of different land-use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soils under three land-use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land-use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land-use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.

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Effects of Microbial Consortia, Applied as Fertilizer Coating, on Soil and Rhizosphere Microbial Communities and Potato Yield

Frontiers in Agronomy ◽

10.3389/fagro.2021.714700 ◽

2021 ◽

Vol 3 ◽

Author(s):

William Overbeek ◽

Thomas Jeanne ◽

Richard Hogue ◽

Donald L. Smith

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Soil Microbial Community ◽

Microbial Community Composition ◽

Bulk Soil ◽

Microbial Inoculants ◽

Flowering Stage ◽

Soil Microbial ◽

Soil Microbial Community Composition

The use of biological inputs in crop production systems, as complements to synthetic inputs, is gaining popularity in the agricultural industry due to increasing consumer demand for more environmentally friendly agriculture. An approach to meeting this demand is the inoculation of field crops with beneficial microbes to promote plant growth and resistance to biotic and abiotic stresses. However, the scientific literature reports inconsistent results following applications of bio-inoculant to fields. The effects of inoculation with beneficial microbes on bulk soil and rhizospheric microbial communities is often overlooked as precise monitoring of soil microbial communities is difficult. The aim of this research was to use Illumina high throughput sequencing (HTS) to shed light on bulk soil and rhizospheric microbial community responses to two commercial microbial inoculants coated onto fertilizer granules, applied to potato fields. Bulk soil samples were collected 4 days before seeding (May 27th), 7 days after seeding (June 7th), at potato shoot emergence (June 21st) and at mid-flowering (July 26th). Rhizospheric soil was collected at the mid-flowering stage. The Illumina MiSeq HTS results indicated that the bulk soil microbial community composition, especially prokaryotes, changed significantly across potato growth stages. Microbial inoculation did not affect bulk soil or rhizospheric microbial communities sampled at the mid-flowering stage. However, a detailed analysis of the HTS results showed that bulk soil and rhizospheric microbial community richness and composition were different for the first treatment block compared to the other three blocks. The spatial heterogeneity of the soil microbial community between blocks of plots was associated with potato tuber yield changes, indicating links between crop productivity and soil microbial community composition. Understanding these links could help in production of high-quality microbial inoculants to promote potato productivity.

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Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Microbiome ◽

10.1186/s40168-021-01042-9 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Javier A. Ceja-Navarro ◽

Yuan Wang ◽

Daliang Ning ◽

Abelardo Arellano ◽

Leila Ramanculova ◽

...

Keyword(s):

Community Composition ◽

Community Assembly ◽

Panicum Virgatum ◽

Large Scale ◽

Rhizosphere Soil ◽

Bacterial Community Composition ◽

Temporal Variations ◽

Bulk Soil ◽

Growth Stages ◽

Soil System

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants (Panicum virgatum) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

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Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

Frontiers in Microbiology ◽

10.3389/fmicb.2013.00177 ◽

2013 ◽

Vol 4 ◽

Cited By ~ 30

Author(s):

Xuefeng Peng ◽

Amal Jayakumar ◽

Bess B. Ward

Keyword(s):

Community Composition ◽

Oxygen Minimum Zones ◽

Ammonia Oxidizing Archaea ◽

Oxygen Minimum

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Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments

Applied and Environmental Microbiology ◽

10.1128/aem.02806-08 ◽

2009 ◽

Vol 75 (10) ◽

pp. 3127-3136 ◽

Cited By ~ 120

Author(s):

Martina Herrmann ◽

Aaron M. Saunders ◽

Andreas Schramm

Keyword(s):

Community Composition ◽

Plant Species ◽

Trophic Status ◽

Gene Diversity ◽

Freshwater Sediments ◽

Lake Trophic Status ◽

Ammonia Oxidizing Archaea ◽

Softwater Lakes ◽

Species Specific ◽

Pcr Targeting

ABSTRACT Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like L. uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions.

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Archaea Are the Major Responsive Ammonia Oxidizers in a Paddy Soil Following Fertilization and Irrigation

10.21203/rs.3.rs-130507/v1 ◽

2020 ◽

Author(s):

Limin Wang ◽

Dongfeng Huang

Keyword(s):

Community Composition ◽

Ammonia Oxidation ◽

Chemical Properties ◽

Paddy Soils ◽

Environmental Drivers ◽

Soil Nitrification ◽

Treated Soil ◽

Ammonia Oxidizing Archaea ◽

Traditional Irrigation ◽

Almost All

Abstract Because ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their specific environmental drivers in paddy soils under different fertilization and irrigation regimes remains unclear. In this study, we investigated archaeal abundance, activity and community composition in acid paddy soils by a 10-year field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 µg NO2−-N g− 1 d.w.day− 1) was found in T2 (optimal irrigation and fertilization) - treated soils, whereas the lowest PAO (0.004 µg NO2−-N g− 1 d.w.day− 1) in T0 (traditional irrigation)- treated soils. Compared with the T0 - treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2 - treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The archaeal phylum Crenarchaeota and genus Candidatus Nitrosotalea were mainly found in the T2-treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Together, our findings confirmed that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain optimum rice yields in a subtropical paddy field.

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