scholarly journals Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

2021 ◽  
Author(s):  
Jun Zhao ◽  
Baozhan Wang ◽  
Xue Zhou ◽  
Mohammad Saiful Alam ◽  
Jianbo Fan ◽  
...  
Keyword(s):  
Community Composition ◽  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Agricultural Soils ◽  
Terrestrial Ecosystems ◽  
Low Ph ◽  
Ph Change ◽  
Monooxygenase Gene ◽  
Ammonia Oxidising Archaea

AbstractAmmonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.

scholarly journals Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans

2020 ◽  
Vol 11 ◽  
Author(s):  
Yaping Wang ◽  
Guihao Li ◽  
Fei Shi ◽  
Jun Dong ◽  
Eleni Gentekaki ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Community Composition ◽  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Regional Scale ◽  
Negative Relationship ◽  
Rrna Gene ◽  
Functional Composition ◽  
Coastal Oceans ◽  
Limiting Nutrients

Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentration of dissolved oxygen (DO). These two factors also significantly co-varied with the OTU-based community composition of P/NEs. The effect of geographic distance on community composition of P/NEs was negligible. Among the three functional groups defined by trophic traits, heterotrophs had the highest OTU richness, which exhibited a U-shaped relationship with both DO and Chl-a. The community of P/NEs was dominated by heterotrophs and mixotrophs in terms of read numbers, which showed a trade-off along the gradient of phosphate, but no significant changes along DO and Chl-a gradients, indicating functional redundancy. Similarly, the proportion of phototrophs was significantly and positively correlated with the concentration of silicate. Our results indicate that taxonomic and functional composition of P/NEs are decoupled on a regional scale, and limiting nutrients are important factors in modulating functional composition of these microorganisms in the studied area. These findings contribute toward gaining a better understanding of how diversity of small eukaryotes and their functions are structured in coastal oceans and the effect of environmental changes on the structuring process.

scholarly journals Convergent modelling of past soil organic carbon stocks but divergent projections

2015 ◽  
Vol 12 (14) ◽  
pp. 4373-4383 ◽  
Author(s):  
Z. Luo ◽  
E. Wang ◽  
H. Zheng ◽  
J. A. Baldock ◽  
O. J. Sun ◽  
...  
Keyword(s):  
Field Experiments ◽  
Environmental Changes ◽  
Agricultural Soils ◽  
Terrestrial Ecosystems ◽  
C Sequestration ◽  
Biogeochemical Model ◽  
Data Set ◽  
Soil C ◽  
C Stocks ◽  
Drying Conditions

Abstract. Soil carbon (C) models are important tools for understanding soil C balance and projecting C stocks in terrestrial ecosystems, particularly under global change. The initialization and/or parameterization of soil C models can vary among studies even when the same model and data set are used, causing potential uncertainties in projections. Although a few studies have assessed such uncertainties, it is yet unclear what these uncertainties are correlated with and how they change across varying environmental and management conditions. Here, applying a process-based biogeochemical model to 90 individual field experiments (ranging from 5 to 82 years of experimental duration) across the Australian cereal-growing regions, we demonstrated that well-designed optimization procedures enabled the model to accurately simulate changes in measured C stocks, but did not guarantee convergent forward projections (100 years). Major causes of the projection uncertainty were due to insufficient understanding of how microbial processes and soil C pool change to modulate C turnover. For a given site, the uncertainty significantly increased with the magnitude of future C input and years of the projection. Across sites, the uncertainty correlated positively with temperature but negatively with rainfall. On average, a 331 % uncertainty in projected C sequestration ability can be inferred in Australian agricultural soils. This uncertainty would increase further if projections were made for future warming and drying conditions. Future improvement in soil C modelling should focus on how the microbial community and its C use efficiency change in response to environmental changes, and better conceptualization of heterogeneous soil C pools and the C transformation among those pools.

scholarly journals From Water into Sediment—Tracing Freshwater Cyanobacteria via DNA Analyses

2021 ◽  
Vol 9 (8) ◽  
pp. 1778
Author(s):  
Ebuka Canisius Nwosu ◽  
Patricia Roeser ◽  
Sizhong Yang ◽  
Lars Ganzert ◽  
Olaf Dellwig ◽  
...  
Keyword(s):  
Water Column ◽  
High Throughput Sequencing ◽  
Surface Sediments ◽  
Environmental Changes ◽  
Sediment Traps ◽  
Sequence Variant ◽  
Sediment Record ◽  
Term Monitoring ◽  
Taphonomic Processes

Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May–October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.

scholarly journals Structural and Functional Shift in Soil Bacterial Community in Response to Long-Term Compost Amendment in Paddy Field

2021 ◽  
Vol 11 (5) ◽  
pp. 2183
Author(s):  
Sookjin Kim ◽  
Sandipan Samaddar ◽  
Poulami Chatterjee ◽  
Aritra Roy Choudhury ◽  
Jeongyun Choi ◽  
...  
Keyword(s):  
Community Composition ◽  
Management Practices ◽  
Agricultural Soils ◽  
Growth Promotion ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Soil Bacterial Diversity ◽  
Compost Amendment ◽  
Soil Bacterial

Microbial community composition and diversity of agricultural soils primarily depend on management practices. The application of compost on agricultural fields is known to increase soil fertility, which can also help to enhance agricultural productivity. The effects of long-term application of compost along with nitrogen (N), phosphorus (P), and potassium (K) (+Compost) on soil bacterial diversity and community profiles were assessed by amplicon sequencing targeting the 16S rRNA gene of bacteria and compared with those on soils that received only NPK but not compost (−Compost). Ordination plot showed treatments to cluster differently, implying changes in community composition, which were validated with taxonomical data showing Firmicutes, Actinobacteria, and their related classes to be significantly higher in +Compost than in −Compost soils. The predicted abundance of functional genes related to plant growth promotion, development, and decomposition was significantly higher in compost-amended soil than in soils without compost. The results are of particular importance as they provide insights into designing management practices to promote agricultural sustainability.

scholarly journals Convergent modeling of past soil organic carbon stocks but divergent projections

2015 ◽  
Vol 12 (5) ◽  
pp. 4245-4272 ◽  
Author(s):  
Z. Luo ◽  
E. Wang ◽  
H. Zheng ◽  
J. A. Baldock ◽  
O. J. Sun ◽  
...  
Keyword(s):  
Soil Carbon ◽  
Field Experiments ◽  
Environmental Changes ◽  
Agricultural Soils ◽  
Terrestrial Ecosystems ◽  
Turnover Time ◽  
Carbon Stocks ◽  
Biogeochemical Model ◽  
Carbon Modeling ◽  
Carbon Composition

Abstract. Soil carbon models are important tool to understand soil carbon balance and project carbon stocks in terrestrial ecosystems, particularly under global change. The initialization and/or parameterization of soil carbon models can vary among studies even when the same model and dataset are used, causing potential uncertainties in projections. Although a few studies have assessed such uncertainties, it is yet unclear what these uncertainties are correlated with and how they change across varying environmental and management conditions. Here, applying a process-based biogeochemical model to 90 individual field experiments (ranging from 5 to 82 years of experimental duration) across the Australian cereal-growing regions, we demonstrated that well-designed calibration procedures enabled the model to accurately simulate changes in measured carbon stocks, but did not guarantee convergent forward projections (100 years). Major causes of the projection uncertainty were due to insufficient understanding of how microbial processes and soil carbon composition change to modulate carbon turnover. For a given site, the uncertainty significantly increased with the magnitude of future carbon input and years of the projection. Across sites, the uncertainty correlated positively with temperature, but negatively with rainfall. On average, a 331% uncertainty in projected carbon sequestration ability can be inferred in Australian agricultural soils. This uncertainty would increase further if projections were made for future warming and drying conditions. Future improvement in soil carbon modeling should focus on how microbial community and its carbon use efficiency change in response to environmental changes, better quantification of composition of soil carbon and its change, and how the soil carbon composition will affect its turnover time.

scholarly journals A case of long-term herbivory: specialized feeding trace on Parrotia (Hamamelidaceae) plant species

2020 ◽  
Vol 7 (10) ◽  
pp. 201449
Author(s):  
Benjamin Adroit ◽  
Xin Zhuang ◽  
Torsten Wappler ◽  
Jean-Frederic Terral ◽  
Bo Wang
Keyword(s):  
Western Europe ◽  
Environmental Changes ◽  
Terrestrial Ecosystems ◽  
Insect Damage ◽  
Ecosystem Structure ◽  
Biogeographic History ◽  
Fossil Leaves ◽  
Continuous Presence ◽  
Insect Interactions

Interactions between plants and insects evolved during millions of years of coevolution and maintain the trophic balance of terrestrial ecosystems. Documenting insect damage types (DT) on fossil leaves is essential for understanding the evolution of plant–insect interactions and for understanding the effects of major environmental changes on ecosystem structure. However, research focusing on palaeoherbivory is still sparse and only a tiny fraction of fossil leaf collections have been analysed. This study documents a type of insect damage found exclusively on the leaves of Parrotia species (Hamamelidaceae). This DT was identified on Parrotia leaves from Willershausen (Germany, Pliocene) and from Shanwang (China, Miocene) and on their respective endemic modern relatives: Parrotia perisca in the Hyrcanian forests (Iran) and Parrotia subaequalis in the Yixing forest (China). Our study demonstrates that this insect DT persisted over at least 15 Myr spanning eastern Asia to western Europe. Against expectations, more examples of this type of herbivory were identified on the fossil leaves than on the modern examples. This mismatch may suggest a decline of this specialized plant–insect interaction owing to the contraction of Parrotia populations in Eurasia during the late Cenozoic. However, the continuous presence of this DT demonstrates a robust and long-term plant–herbivore association, and provides new evidence for a shared biogeographic history of the two host plants.

Integrated long-term responses of an arctic–alpine willow and associated ectomycorrhizal fungi to an altered environment

2006 ◽  
Vol 84 (5) ◽  
pp. 831-843 ◽  
Author(s):  
Karina E. Clemmensen ◽  
Anders Michelsen
Keyword(s):  
Community Composition ◽  
Field Experiments ◽  
Environmental Changes ◽  
Plant Biomass ◽  
The Arctic ◽  
Root Tip ◽  
Root Mass ◽  
Cenococcum Geophilum ◽  
Root Tips

We evaluated ectomycorrhizal (ECM) colonization and morphotype community composition together with growth response and biomass distribution in the arctic–alpine, prostrate willow Salix herbacea L. × Salix polaris Wahlenb. after 11 seasons of shading, warming, and fertilization at a fellfield in subarctic Sweden. The aim was to assess responses of the integrated plant–fungal system to long-term field experiments simulating expected environmental changes. Warming more than doubled aboveground S. herbacea × S. polaris biomass and shoot growth, whereas shading and nutrient addition had less influence on these variables. In shaded plants, adjustments at leaf level probably buffered major changes in plant biomass allocation. Fertilization increased the root mass fraction and changed root system morphology by decreasing the number of root tips per unit root mass. While no long-term changes in total ECM colonization (%ECM root tips) in response to the treatments were identified, ECM colonization in June just after snowmelt was positively correlated with root density. Changes in densities of potential host plants may therefore be of great importance for ECM colonization intensity in this ecosystem type. The ECM morphotype community changed through the season, and frequencies of some ECM morphotypes ( Cortinarius saturninus and Clavulina spp.) changed more with season than with the treatments. Warming only slightly affected ECM morphotype frequencies, which implies a balanced increase in root tip numbers of most ECM morphotypes in warmed plants. Fertilization changed ECM morphotype community composition mainly because of a decrease in Cenococcum geophilum frequency and an increase in Tomentella stuposa frequency. We hypothesize that a shift from drought stress-tolerant fungi towards a dominance of minerogenic fungi may take place if nutrient availability increases substantially because of anthropogenic disturbances.

scholarly journals Evidence from South Africa for a protracted end-Permian extinction on land

2021 ◽  
Vol 118 (17) ◽  
pp. e2017045118
Author(s):  
Pia A. Viglietti ◽  
Roger B. J. Benson ◽  
Roger M. H. Smith ◽  
Jennifer Botha ◽  
Christian F. Kammerer ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Terrestrial Ecosystems ◽  
Faunal Assemblage ◽  
Karoo Basin ◽  
Extinction Rates ◽  
Occurrence Data ◽  
Permian Extinction ◽  
Assemblage Zone ◽  
Long Term Trend

Earth’s largest biotic crisis occurred during the Permo–Triassic Transition (PTT). On land, this event witnessed a turnover from synapsid- to archosauromorph-dominated assemblages and a restructuring of terrestrial ecosystems. However, understanding extinction patterns has been limited by a lack of high-precision fossil occurrence data to resolve events on submillion-year timescales. We analyzed a unique database of 588 fossil tetrapod specimens from South Africa’s Karoo Basin, spanning ∼4 My, and 13 stratigraphic bin intervals averaging 300,000 y each. Using sample-standardized methods, we characterized faunal assemblage dynamics during the PTT. High regional extinction rates occurred through a protracted interval of ∼1 Ma, initially co-occurring with low origination rates. This resulted in declining diversity up to the acme of extinction near the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary. Regional origination rates increased abruptly above this boundary, co-occurring with high extinction rates to drive rapid turnover and an assemblage of short-lived species symptomatic of ecosystem instability. The “disaster taxon” Lystrosaurus shows a long-term trend of increasing abundance initiated in the latest Permian. Lystrosaurus comprised 54% of all specimens by the onset of mass extinction and 70% in the extinction aftermath. This early Lystrosaurus abundance suggests its expansion was facilitated by environmental changes rather than by ecological opportunity following the extinctions of other species as commonly assumed for disaster taxa. Our findings conservatively place the Karoo extinction interval closer in time, but not coeval with, the more rapid marine event and reveal key differences between the PTT extinctions on land and in the oceans.

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