Grassland Management Regimens Reduce Small-Scale Heterogeneity and Species Diversity of β-Proteobacterial Ammonia Oxidizer Populations

ABSTRACT The impact of soil management practices on ammonia oxidizer diversity and spatial heterogeneity was determined in improved (addition of N fertilizer), unimproved (no additions), and semi-improved (intermediate management) grassland pastures at the Sourhope Research Station in Scotland. Ammonia oxidizer diversity within each grassland soil was assessed by PCR amplification of microbial community DNA with both ammonia oxidizer-specific, 16S rRNA gene (rDNA) and functional, amoA, gene primers. PCR products were analysed by denaturing gradient gel electrophoresis, phylogenetic analysis of partial 16S rDNA and amoA sequences, and hybridization with ammonia oxidizer-specific oligonucleotide probes. Ammonia oxidizer populations in unimproved soils were more diverse than those in improved soils and were dominated by organisms representing Nitrosospira clusters 1 and 3 and Nitrosomonas cluster 7 (closely related phylogenetically to Nitrosomonas europaea). Improved soils were only dominated by Nitrosospira cluster 3 and Nitrosomonas cluster 7. These differences were also reflected in functional gene (amoA) diversity, with amoA gene sequences of both Nitrosomonas and Nitrosospira species detected. Replicate 0.5-g samples of unimproved soil demonstrated significant spatial heterogeneity in 16S rDNA-defined ammonia oxidizer clusters, which was reflected in heterogeneity in ammonium concentration and pH. Heterogeneity in soil characteristics and ammonia oxidizer diversity were lower in improved soils. The results therefore demonstrate significant effects of soil management on diversity and heterogeneity of ammonia oxidizer populations that are related to similar changes in relevant soil characteristics.

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Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment

Applied and Environmental Microbiology ◽

10.1128/aem.00595-10 ◽

2010 ◽

Vol 76 (22) ◽

pp. 7626-7634 ◽

Cited By ~ 136

Author(s):

Nejc Stopnišek ◽

Cécile Gubry-Rangin ◽

Špela Höfferle ◽

Graeme W. Nicol ◽

Ines Mandič-Mulec ◽

...

Keyword(s):

Ammonia Oxidation ◽

Denaturing Gradient Gel Electrophoresis ◽

Inorganic Nitrogen ◽

Peat Soil ◽

Selective Advantage ◽

Ammonia Oxidizer ◽

Ammonium Concentration ◽

Rrna Gene ◽

Ammonia Oxidizers ◽

Ammonia Release

ABSTRACT Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and “deep peat” lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

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The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Frontiers in Microbiology ◽

10.3389/fmicb.2020.574815 ◽

2020 ◽

Vol 11 ◽

Author(s):

João Pereira Santos ◽

António G. G. Sousa ◽

Hugo Ribeiro ◽

Catarina Magalhães

Keyword(s):

Ammonia Oxidation ◽

Estuarine Sediments ◽

Ammonia Oxidizer ◽

Rrna Gene ◽

Ammonia Oxidizing Bacteria ◽

Salinity Regime ◽

Salinity Fluctuation ◽

Ammonia Oxidizing Archaea ◽

Negative Effect ◽

The Impact

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

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First Report of Witches'-Broom Disease of Chinese Wingnut in China and its Association with a Phytoplasma of Aster Yellows Group (16SrI)

Plant Disease ◽

10.1094/pd-89-0529c ◽

2005 ◽

Vol 89 (5) ◽

pp. 529-529 ◽

Cited By ~ 1

Author(s):

Q. Liu ◽

Q. Sun ◽

T. Wu ◽

R. E. Davis ◽

Y. Zhao

Keyword(s):

16S Rdna ◽

Biological Diversity ◽

Nucleotide Sequence Analysis ◽

Soil Drought ◽

Rrna Gene ◽

Polymorphism Analysis ◽

First Report ◽

Broom Disease ◽

The Impact ◽

Chinese Wingnut

Pterocarya stenoptera C. DC., commonly known as Chinese wingnut, is a fast-growing deciduous tree with tough bark and attractive foliage. Because of its tolerance of compact and nutritionally poor soil, drought, and heat, Chinese wingnut is an important component of the biological diversity in natural ecosystems and is a favorable shade tree in China. Chinese wingnut has also been used as a rootstock for walnuts because of its high resistance to soilborne Phytophthora spp. In the spring of 2004, a disease characterized by witches'-broom symptoms was observed affecting Chinese wingnut trees growing in suburban Taian, Shandong, China. The diseased trees developed dense clusters of highly proliferating branches with shortened internodes, leaves on the affected branches were significantly smaller, and some branches and twigs suffered dieback. Phytoplasma infection was suspected as the cause of this Chinese wingnut witches'-broom (CWWB) disease because the disease occurred in an area where phytoplasmal diseases, such as paulownia witches'-broom (PaWB) and jujube witches'-broom (JWB), are common (3). Nested polymerase chain reactions (PCR) were performed on DNA samples extracted from leaves of six diseased trees using phytoplasma-universal 16S rDNA primers (R16mF2/R16mR1 and R16F2n/ R16R2) (1,2). Results revealed that all diseased trees examined were infected by phytoplasma, whereas PCR assays of leaf samples from two nearby symptomless Chinese wingnut trees were negative. Subsequent restriction fragment length polymorphism analysis of the PCR-amplified 16S rDNA indicated that all diseased trees contained the same phytoplasma and that the CWWB phytoplasma belongs to subgroup B of the “Candidatus Phytoplasma asteris” (AY) group (16SrI). Nucleotide sequence analysis of a 16S rRNA gene cloned from CWWB phytoplasma (GenBank Accession No. AY831966) suggested that this phytoplasma is closely related to, but distinct from, PaWB phytoplasma, another member of group16SrI. To our knowledge, this is the first report of Chinese wingnut witches'-broom disease and of its association with a phytoplasma. Further work is being undertaken to examine the ecological and evolutionary relationship between CWWB phytoplasma and other phytoplasmas in the region and to assess the impact of CWWB on walnut rootstock selection. References: (1) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996. (3) S. Zhu et al. Acta Hortic. 472:701, 1998.

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Tracer Dispersion through Karst Conduit: Assessment of Small-Scale Heterogeneity by Multi-Point Tracer Test and CFD Modeling

Hydrology ◽

10.3390/hydrology8040168 ◽

2021 ◽

Vol 8 (4) ◽

pp. 168

Author(s):

Romain Deleu ◽

Sandra Soarez Frazao ◽

Amaël Poulain ◽

Gaëtan Rochez ◽

Vincent Hallet

Keyword(s):

Spatial Heterogeneity ◽

Single Point ◽

Tracer Tests ◽

Tracer Test ◽

Breakthrough Curves ◽

Cfd Modeling ◽

Small Scale ◽

Tracer Concentration ◽

Tracer Dispersion ◽

The Impact

Tracer tests are widely used for characterizing hydrodynamics, from stream-scale to basin-wide scale. In karstic environments, the positioning of field fluorometers (or sampling) is mostly determined by the on-site configuration and setup difficulties. Most users are probably aware of the importance of this positioning for the relevance of data, and single-point tests are considered reliable. However, this importance is subjective to the user and the impact of positioning is not well quantified. This study aimed to quantify the spatial heterogeneity of tracer concentration through time in a karstic environment, and its impact on tracer test results and derived information on local hydrodynamics. Two approaches were considered: on-site tracing experiments in a karstic river, and Computational Fluid Dynamics (CFD) modeling of tracer dispersion through a discretized karst river channel. A comparison between on-site tracer breakthrough curves and CFD results was allowed by a thorough assessment of the river geometry. The results of on-site tracer tests showed significant heterogeneities of the breakthrough curve shape from fluorometers placed along a cross-section. CFD modeling of the tracer test through the associated discretized site geometry showed similar heterogeneity and was consistent with the positioning of on-site fluorometers, thus showing that geometry is a major contributor of the spatial heterogeneity of tracer concentration through time in karstic rivers.

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Comparative Diversity of Ammonia Oxidizer 16S rRNA Gene Sequences in Native, Tilled, and Successional Soils

Applied and Environmental Microbiology ◽

10.1128/aem.65.7.2994-3000.1999 ◽

1999 ◽

Vol 65 (7) ◽

pp. 2994-3000 ◽

Cited By ~ 173

Author(s):

Mary Ann Bruns ◽

John R. Stephen ◽

George A. Kowalchuk ◽

James I. Prosser ◽

Eldor A. Paul

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

16S Rdna ◽

Ammonia Oxidizer ◽

Most Probable Number ◽

Rrna Gene ◽

Probable Number ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Native Soils

ABSTRACT Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes forNitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospiracluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.

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Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor

Applied and Environmental Microbiology ◽

10.1128/aem.02345-20 ◽

2020 ◽

Author(s):

Heidi M.-L. Wipf ◽

Ling Xu ◽

Cheng Gao ◽

Hannah B. Spinner ◽

John Taylor ◽

...

Keyword(s):

Microbial Diversity ◽

Soil Health ◽

Soil Management ◽

Soil Microbiome ◽

Rrna Gene ◽

Microbial Composition ◽

Cover Cropping ◽

And Function ◽

The Impact ◽

Plant Microbiome

Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California’s San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops. Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.

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Soil microbial responses to passive restoration strategies in drylands: a temporal comparison of soil biodiversity and ecosystem function

10.5194/egusphere-egu21-16398 ◽

2021 ◽

Author(s):

Jana Stewart ◽

Nathali Machado de Lima ◽

Richard Kingsford ◽

Miriam Muñoz-Rojas

Keyword(s):

Climate Change ◽

Environmental Indicators ◽

Ecosystem Functions ◽

Rrna Gene ◽

Research Station ◽

Microbial Composition ◽

Soil Biodiversity ◽

Passive Restoration ◽

The Impact ◽

Over Time

<p>Arid and semi-arid (from hereafter dryland) ecosystems cover 70% of Australia, with climate change set to increase this area through desertification. Increased temperatures and reduced water availability are compounded through agricultural overgrazing. This degradation and habitat loss has led to biodiversity loss which disrupts the biogeochemical cycles that maintain these environments, creating a negative feedback loop, and making restoration efforts largely unsuccessful. With soil microbes being important drivers in dryland systems, understanding how different stressors impact the soil biome is needed to improve conservation and restoration efforts and promote resilience and resistance to climate change. Particularly lacking is understanding of these interactions over time.</p><p>Fowlers Gap Research Station is the only research station in the arid zone of Australia and was a working sheep station until 2019. Due to agricultural overgrazing the site is largely degraded however exclusion zones have been set up on the property ranging in time from 3 years to 40 years. These exclusion zones provide a powerful comparison for the impact of soil degradation on drylands. To investigate the impact of overgrazing on the soil biodiversity and ecosystem functions, we selected three of the exclusion zones paired with three degraded sites directly outside of the exclusion zone to assess their microbial composition and functional diversity, along with soil physicochemical properties. We aim to build 16S rRNA gene libraries and co-relate them with the soil chemical variables, to assess the impact of overgrazing on these microbial communities and the ecosystem functions they provide. This knowledge can be used to improve monitoring of conservation and restoration initiatives by providing environmental indicators for soil health over time.</p>

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Can Values of Honesty, Hard Work, Loyalty and Discipline Predict Entrepreneurial Orientation of Muslim Owner Managers?

Journal of Emerging Economies and Islamic Research ◽

10.24191/jeeir.v3i1.9049 ◽

2015 ◽

Vol 3 (1) ◽

pp. 31 ◽

Cited By ~ 2

Author(s):

Rohani Mohd ◽

Badrul Hisham Kamaruddin ◽

Khulida Kirana Yahya ◽

Elias Sanidas

Keyword(s):

Entrepreneurial Orientation ◽

Two Dimensions ◽

Hard Work ◽

Small Scale ◽

Sampling Frame ◽

Policy Makers ◽

Learning Institutions ◽

Innovative Orientation ◽

The Impact ◽

True Values

The purpose of the present study is twofold: first, to investigate the true values of Muslim owner managers; second, to examine the impact of these values on entrepreneurial orientations of Muslim small-scale entrepreneurs. 850 Muslim owner managers were selected randomly using the sampling frame provided by MajlisAmanah Rakyat Malaysia (MARA). 162 completed questionnaires were collected and analyzed. For this paper only two dimensions of entrepreneurial orientations were analyzed: proactive orientation and innovative orientation. Interestingly, the findings revealed that Muslim businessmen/women are honest, loyal, disciplined and hard working. Loyalty and honesty are positively related to proactive orientation, while discipline and hard-work are positively related to innovative orientation. The findings provide implications for existing relevant theories, policy makers, practitioners and learning institutions.

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Land Subsidence Estimation for Aquifer Drainage Induced by Underground Mining

Energies ◽

10.3390/en14154658 ◽

2021 ◽

Vol 14 (15) ◽

pp. 4658

Author(s):

Artur Guzy ◽

Wojciech T. Witkowski

Keyword(s):

Environmental Impact ◽

Land Subsidence ◽

Field Data ◽

Underground Mining ◽

Small Scale ◽

Aquifer System ◽

Maximum Value ◽

The Impact ◽

Method Model ◽

Impact Of Mining

Land subsidence caused by groundwater withdrawal induced by mining is a relatively unknown phenomenon. This is primarily due to the small scale of such movements compared to the land subsidence caused by deposit extraction. Nonetheless, the environmental impact of drainage-related land subsidence remains underestimated. The research was carried out in the “Bogdanka” coal mine in Poland. First, the historical impact of mining on land subsidence and groundwater head changes was investigated. The outcomes of these studies were used to construct the influence method model. With field data, our model was successfully calibrated and validated. Finally, it was used for land subsidence estimation for 2030. As per the findings, the field of mining exploitation has the greatest land subsidence. In 2014, the maximum value of the phenomenon was 0.313 cm. However, this value will reach 0.364 m by 2030. The spatial extent of land subsidence caused by mining-induced drainage extends up to 20 km beyond the mining area’s boundaries. The presented model provided land subsidence patterns without the need for a complex numerical subsidence model. As a result, the method presented can be effectively used for land subsidence regulation plans considering the impact of mining on the aquifer system.

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Foreign investment in emerging legal medicinal cannabis markets: the Jamaica case study

Globalization and Health ◽

10.1186/s12992-021-00687-3 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Marta Rychert ◽

Machel Anthony Emanuel ◽

Chris Wilkins

Keyword(s):

Civil Society ◽

Foreign Investment ◽

Production Efficiency ◽

Production Quality ◽

Small Scale ◽

Organic Cultivation ◽

Enhanced Production ◽

Political Interference ◽

Medicinal Cannabis ◽

The Impact

Abstract Introduction The establishment of a legal market for medicinal cannabis under the Dangerous Drugs Amendment Act 2015 has positioned Jamaica at the forefront of cannabis law reform in the developing world. Many local cannabis businesses have attracted investment from overseas, including from Canada, US and Europe. Aim To explore the opportunities and risks of foreign investment in an emerging domestic legal cannabis market in a developing country. Methods Thematic analysis of semi-structured face-to-face interviews with 22 key informants (KIs) from the Jamaican government, local cannabis industry, academia and civil society, and field observations of legal and illegal cannabis cultivators. Results KIs from the Jamaican public agencies and domestic cannabis entrepreneurs saw foreign investment as an essential source of capital to finance the start-up costs of legal cannabis businesses. Local cannabis entrepreneurs prioritised investors with the greatest financial resources, brand reputation and export networks. They also considered how allied an investor was with their business vision (e.g., organic cultivation, medical vs. recreational). The key benefits of partnering with a foreign investor included transfer of technical knowledge and financial capital, which enhanced production, quality assurance and seed-to-sale tracking. Some KIs expressed concern over investors’ focus on increasing production efficiency and scale at the expense of funding research and development (R&D) and clinical trials. KIs from the local industry, government agencies and civil society highlighted the risks of ‘predatory’ shareholder agreements and domestic political interference. Concerns were raised about the impact of foreign investment on the diversity of the domestic cannabis sector in Jamaica, including the commitment to transition traditional illegal small-scale cannabis cultivators to the legal sector. Conclusion While foreign investment has facilitated the commercialisation of the cannabis sector in Jamaica, regulatory measures are also needed to protect the domestic industry and support the transition of small-scale illegal cultivators to the legal regime. Foreign investments may alter the economic, social and political determinants of health in transitioning from illegal to legal cannabis market economy.

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