Ecological niche differentiation of ammonia-oxidising archaea and bacteria in acidic soils due to land use change

Soil Research ◽  
2018 ◽  
Vol 56 (1) ◽  
pp. 71 ◽  
Author(s):  
Shenyan Dai ◽  
Qian Liu ◽  
Jun Zhao ◽  
Jinbo Zhang
Keyword(s):  
Land Use ◽  
Ecological Niche ◽  
Ammonia Oxidation ◽  
Agricultural Soils ◽  
Niche Differentiation ◽  
Stable Isotope Probing ◽  
Paddy Soils ◽  
Acidic Soils ◽  
Moisture Condition ◽  
Ammonia Oxidising Archaea

Nitrification can be driven by either ammonia-oxidising bacteria (AOB) or ammonia-oxidising archaea (AOA) and is a central process in the nitrogen cycle. However, to date, it is not clear how the ecological niche differentiation of AOB and AOA are affected by land use and management changes in strongly acidic soils in subtropical China. In this study, three different land-use acidic soils – forest, upland, and paddy soils – were collected and a DNA Stable-Isotope Probing experiment performed to determine the relative contributions of AOA and AOB to ammonia oxidation in these soils. The results showed that AOA, but not AOB, amoA genes were detected in 13C-labelled DNA in the forest and paddy soils; however, only AOB amoA genes were detected in 13C-labelled DNA in the upland agricultural soils. The growth and activity of AOA and AOB in the different land-use soils provided direct evidence for the shift in roles for AOA and AOB in ammonia oxidation. AOA played the predominant role in ammonia oxidation in acidic forest and paddy soils. However, AOB, not AOA, mainly regulated the ammonia oxidation in acidic upland agricultural soils. Phylogenetic analysis indicated that AOA members within the marine Group1.1a-associated lineage dominated nitrification in the forest and paddy soils. Ammonia oxidation in the upland soil was catalysed by Nitrosospira cluster 3-like AOB. The moisture condition was likely the main reason inducing the ecological niche differentiation between upland and paddy soils; and AOA was more suitable for growth in the flooded, low oxygen conditions.

scholarly journals Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary

2021 ◽  
Vol 11 ◽  
Author(s):  
Xinxin Wang ◽  
Lu Lu ◽  
Xue Zhou ◽  
Xiufeng Tang ◽  
Lu Kuang ◽  
...  
Keyword(s):  
Yangtze River ◽  
Ammonia Oxidation ◽  
Agricultural Soils ◽  
River Estuary ◽  
Niche Differentiation ◽  
Yangtze River Estuary ◽  
Ammonia Oxidizing Bacteria ◽  
Community Structures ◽  
Dominant Group ◽  
Clade B

The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.

scholarly journals Abandoned agricultural soils from the central part of the Yamal region of Russia: morphology, diversity, and chemical properties

2020 ◽  
Vol 5 (1) ◽  
pp. 94-106
Author(s):  
Evgeny Abakumov ◽  
Evgeniya Morgun ◽  
Alexandr Pechkin ◽  
Vyacheslav Polyakov
Keyword(s):  
Land Use ◽  
Agricultural Soils ◽  
Anthropogenic Impacts ◽  
Chemical Properties ◽  
Organic Carbon Content ◽  
Active Growth ◽  
Natural Processes ◽  
Agrochemical Properties ◽  
Fallow Lands ◽  
Abandoned Lands

AbstractThe post-anthropogenic and soil cover transformations of former agricultural soils on the abandoned lands in the Russian Arctic territory are poorly investigated due to the active growth of the city complexes and increasing area occupied by agricultural lands. That is lead to an increase in the area of the arable lands surrounding the polar urbanized territories. Today, most of that land allocated for agricultural needs has been abandoned or affected by other types of land use. This study aimed to investigate the abandoned lands surrounding some of the settlements in the central part of the Yamal region. The soil diversity, morphology, and chemical and agrochemical properties were investigated with special reference to the specific transformations that occur to fallow lands under permafrost-affected cryogenic-ecosystem conditions. Analysis of data show that these soils are characterized by features relating to both, previous (and existing), anthropogenic impacts and natural processes such as cryogenic mass transfer. The degradation of the arable humus-enriched horizon was not as pronounced as it has been in more humid boreal environments over recent decades. The organic carbon content in topsoil depends on the land use and varied considerably among the soil types. The former arable topsoil horizon has been stable over time in terms of its morphological features and agrochemical state. Despite the high soil acidity levels, thenutrient content in the anthropogenically impacted soils was still high, even though being abandoned for 20 years.

scholarly journals Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Roxana T. Shafiee ◽  
Poppy J. Diver ◽  
Joseph T. Snow ◽  
Qiong Zhang ◽  
Rosalind E. M. Rickaby
Keyword(s):  
Comparative Genomics ◽  
Trace Metals ◽  
Trace Metal ◽  
Ammonia Oxidation ◽  
Testable Hypothesis ◽  
Niche Separation ◽  
Toxicity Threshold ◽  
Geologic Time ◽  
Additional Explanation ◽  
Ammonia Oxidising Archaea

AbstractAmmonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.

scholarly journals Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Limin Wang ◽  
Dongfeng Huang
Keyword(s):  
Ammonia Oxidation ◽  
Chemical Properties ◽  
Paddy Soils ◽  
Soil Nitrification ◽  
Treated Soil ◽  
Ammonia Oxidizing Archaea ◽  
Rice Yields ◽  
Traditional Irrigation ◽  
Almost All ◽  
And Function

AbstractBecause 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 edaphic drivers in paddy soils under different fertilization and irrigation regimes remain unclear. In this study, we investigated AOA abundance, diversity and activity in acid paddy soils by a field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 μg NO 2 -  –N g-1 d.w.day-1) was found in T2 (optimal irrigation and fertilization)—treated soils, whereas the lowest PAO (0.004 μg NO 2 -  –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 AOA phylum Crenarchaeota was mainly found in the T2—treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Furthermore, the T2 treatment had higher rice yield than the T0 and T1 treatments. Together, our findings confirm that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain rice yields in the present study.

Soil Aggregates Stability of Forest Islands and Adjacent Ecosystems in West Africa

2021 ◽  
Vol 9 (2) ◽  
pp. 283
Author(s):  
Amelie Baomalgré Bougma ◽  
Korodjouma Ouattara ◽  
Halidou Compaore ◽  
Hassan Bismarck Nacro ◽  
Caleb Melenya ◽  
...  
Keyword(s):  
Land Use ◽  
West Africa ◽  
Agricultural Soils ◽  
Direct Action ◽  
Soil Aggregates ◽  
Aggregate Stability ◽  
Mean Annual Precipitation ◽  
Savanna Vegetation ◽  
Study Sites ◽  
Forest Islands

In the more mesic savanna areas of West Africa, many areas of relatively tall and dense vegetation with a species composition more characteristic of forest than savanna are often found around villages areas. These ‘forest islands’ may be the direct action of human activity. To better understand these patches with relatively luxuriant vegetation, our study focused on how they influence soil aggregation in comparison with nearby areas and natural savanna vegetation across a precipitation transect in West Africa for which mean annual precipitation at the study sites ranges from 0.80 to 1.27 m a-1. Soil samples were taken from 0 to 5 cm and 5 to 10 cm depths and aggregate groups with diameters: > 500 μm, 500-250 μm and 250-53 μm (viz. “macroaggregates”, “mesoaggregates” and “microaggregates”) determined using the wet sieving method. The results showed significantly higher proportion of stable meso and macroaggregates in forest islands and natural savanna compared to agricultural soils (p <0.05). On the other hand, although there was no effect of land-use type on microaggregates stability, there was a strong tendency for the microaggregate fraction across all land use types to increase with increasing precipitation. Soil organic carbon and iron oxides contents are the most important factors influencing aggregate stability in West African ecosystems. By increasing soil structural stability, forest islands contribute to soil erosion reduction and the control of land degradation.

scholarly journals Implications of changing from grazed or semi-natural vegetation to forestry for carbon stores and fluxes in upland organo-mineral soils in the UK

2007 ◽  
Vol 11 (1) ◽  
pp. 61-76 ◽  
Author(s):  
B. Reynolds
Keyword(s):  
Land Use ◽  
Organic Carbon ◽  
Best Practice ◽  
Agricultural Soils ◽  
Relative Magnitude ◽  
International Studies ◽  
Best Practice Guidelines ◽  
Carbon Reservoir ◽  
Mineral Soils ◽  
The Uk

Abstract. In the UK, as organo-mineral soils are a significant store of soil organic carbon (SOC), they may become increasingly favoured for the expansion of upland forestry. It is important, therefore, to assess the likely impacts on SOC of this potentially major land use change. Currently, these assessments rely on modelling approaches which assume that afforestation of organo-mineral soils is "carbon neutral". This review evaluates this assumption in two ways. Firstly, UK information from the direct measurement of SOC change following afforestation is examined in the context of international studies. Secondly, UK data on the magnitude and direction of the major fluxes in the carbon cycle of semi-natural upland ecosystems are assessed to identify the likely responses of the fluxes to afforestation of organo-mineral soils. There are few directly relevant measurements of SOC change following afforestation of organo-mineral soils in the UK uplands but there are related studies on peat lands and agricultural soils. Overall, information on the magnitude and direction of change in SOC with afforestation is inconclusive. Data on the accumulation of litter beneath conifer stands have been identified but the extent to which the carbon held in this pool is incorporated into the stable soil carbon reservoir is uncertain. The effect of afforestation on most carbon fluxes is small because the fluxes are either relatively minor or of the same magnitude and direction irrespective of land use. Compared with undisturbed moorland, particulate organic carbon losses increase throughout the forest cycle but the data are exclusively from plantation conifer forests and in many cases pre-date current industry best practice guidelines which aim to reduce such losses. The biggest uncertainty in flux estimates is the relative magnitude of the sink for atmospheric carbon as trees grow and mature compared with that lost during site preparation and harvesting. Given the size of this flux relative to many of the others, this should be a focus for future carbon research on these systems.

scholarly journals Increase soil aggregate stability can limit colloidal phosphorus loss potentials from agricultural systems

2019 ◽  
Author(s):  
Fayong Li ◽  
Xinqiang Liang ◽  
Hua Li ◽  
Yingbin Jin ◽  
Junwei Jin ◽  
...  
Keyword(s):  
Land Use ◽  
Aggregate Stability ◽  
Aggregate Size ◽  
Soil Aggregate ◽  
Paddy Soils ◽  
Total Carbon ◽  
Agricultural Systems ◽  
Soil Aggregate Stability ◽  
Soil P ◽  
Land Use Types

Abstract Background Colloid-facilitated phosphorus (P) transport is a recognized important pathway for soil P loss in agricultural systems, but limited information is available on the soil aggregate-associated colloidal P. To elucidate the effects of aggregate size on the loss potential of colloidal P (P coll ) in agricultural systems, soils (0-20 cm depth) from six land use types were sampled in Zhejiang province in the Yangtz river delta region, China. The aggregate size fractions (2–8 mm, 0.26–2 mm, 0.053–0.26 mm and <0.053 mm) separated by wet-sieving method were analyzed.Results Results showed that the 0.26–2 mm small macroaggregates had the highest total P (TP) content. For acidic soils, the highest P coll content was also found in the 0.26–2 mm aggregate size, while the lowest was found in the <0.053 mm (silt+clay)-sized particles, the opposite of that found in alkaline soils. Paddy soils contained less P coll than other land use types. The P coll in total dissolved P (TDP) was dominated by <0.053 mm (silt+clay)-sized particles. Aggregate size did strongly influence the loss potential of P coll in paddy soils, where P coll contributed up to 83% TDP in the silt+clay sized particles. The P coll content was positively correlated with TP, Al, Fe and mean weight diameter (MWD). Aggregate associated total carbon (TC), total nitrogen (TN), C/P, and C/N had significant, but negative effects on the contribution of P coll to potential soil P losses. The P coll content of the aggregates was controlled by aggregate associated TP and Al content as well as soil pH value, with P coll loss potential from aggregates being controlled by its organic matter content.Conclusion Therefore, we conclude that management practices that increase soil aggregate stability or its organic carbon content will limit P coll loss from agricultural systems.

scholarly journals Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

2020 ◽  
Author(s):  
Marie E. Kroeger ◽  
Laura K. Meredith ◽  
Kyle M. Meyer ◽  
Kevin D. Webster ◽  
Plinio Barbosa de Camargo ◽  
...  
Keyword(s):  
Land Use ◽  
Greenhouse Gas ◽  
Management Practices ◽  
Carbon Sink ◽  
Brazilian Amazon ◽  
Stable Isotope Probing ◽  
Methane Cycling ◽  
Agricultural Conversion ◽  
Land Use Types ◽  
Pasture Conversion

ABSTRACTThe Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink that is threatened by agricultural conversion. Rainforest-to-pasture conversion leads to the release of a potent greenhouse gas by converting soil from a methane sink into a source. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could explain the greater methane flux. Furthermore, we found that secondary rainforests recovered as methane sinks, indicating the potential for reforestation to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

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