Rhizosphere Microbiome Regulates the Growth of Mustard under Organic Greenhouse Cultivation

Organic cultivation can improve soil fertility and biodiversity through the preservation of soil organic matter. Meanwhile, greenhouse cultivation can provide a controlled environment and therefore enables the management of every aspect of plant growth. In recent years, the combination of organic and greenhouse cultivation has slowly become a popular option in tropical regions to prevent the unpredictable impact of weather. Although it is known that organic cultivation significantly increases the density and species of microorganisms, the impact of soil microbiome on short-term vegetable growth under organic greenhouse cultivation is still not elucidated. In this study, we examined soil physiochemical properties as well as the rhizosphere microbiome from healthy and diseased mustard plants under organic greenhouse cultivation. Through next generation sequencing (NGS) analysis, our results revealed that the rhizosphere microbiome structure of healthy mustard plants was significantly different from those of the diseased mustard plants under organic greenhouse cultivation. Our findings suggest that soil microbiome composition can influence the growth of the vegetable significantly. As such, we have shown the impact of soil microbiome on vegetable growth under organic greenhouse cultivation and provide a possible strategy for sustainable agriculture.

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Soil hydrology drives ecological niche differentiation in a native prairie microbiome

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz163 ◽

2019 ◽

Vol 96 (1) ◽

Cited By ~ 2

Author(s):

James S Griffin ◽

Loren A Haug ◽

Vivien A Rivera ◽

Liliana M Hernandez Gonzalez ◽

John J Kelly ◽

...

Keyword(s):

Hydrological Regime ◽

Niche Differentiation ◽

Soil Microbiome ◽

Sand Ridge ◽

Edaphic Factors ◽

Soil Hydrology ◽

Data Set ◽

Microbiome Composition ◽

Terrestrial Environments ◽

The Impact

ABSTRACT While the impacts of soil moisture on soil microbiome diversity and composition are well characterized, the influence of hydrological regime has been overlooked. As precipitation patterns are altered by climate change, understanding the impact of soil hydrology on community structure and function is critical. In this work, water level was continuously monitored for over a year in a Midwestern prairie-wetland at 10 cm depth increments up to a depth of 120 cm in 10 locations. We analyzed microbiome composition and edaphic factors in soil cores collected from this unique spatially distributed, longitudinal data set. We demonstrate that the fraction of time that each sample was inundated explains more variability in diversity and composition across this site than other commonly assessed edaphic factors, such as soil pH or depth. Finally, we show that these compositional changes influence abundance of ammonia oxidizers. The observed patterns in community composition and diversity are fundamentally regulated by the interaction of water with a structured landscape, particularly an elevated sand ridge characterized by drier conditions and a lower-lying wetland with more clayey soils. Similar processes are generally expected to influence the biogeography of many terrestrial environments, as morphology, hydrology and soil properties generally co-vary.

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Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields

Frontiers in Plant Science ◽

10.3389/fpls.2021.806915 ◽

2022 ◽

Vol 12 ◽

Author(s):

Yulduzkhon Abdullaeva ◽

Stefan Ratering ◽

Binoy Ambika Manirajan ◽

David Rosado-Porto ◽

Sylvia Schnell ◽

...

Keyword(s):

Host Plant ◽

Vertical Transmission ◽

Plant Traits ◽

Aegilops Tauschii ◽

Seed Transmission ◽

Rrna Gene ◽

Wheat Species ◽

Microbiome Composition ◽

Rhizosphere Microbiome ◽

The Impact

The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank’s and seed-originated microbiome recruitment depend on both plants’ genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.

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Evaluating Forest Cover and Fragmentation in Costa Rica with a Corrected Global Tree Cover Map

Remote Sensing ◽

10.3390/rs12193226 ◽

2020 ◽

Vol 12 (19) ◽

pp. 3226

Author(s):

Daniel Cunningham ◽

Paul Cunningham ◽

Matthew E. Fagan

Keyword(s):

Costa Rica ◽

Forest Cover ◽

Agricultural Land ◽

Forest Area ◽

Tree Cover ◽

Agricultural Crop ◽

Forest Change ◽

Alos Palsar ◽

Tropical Regions ◽

The Impact

Global tree cover products face challenges in accurately predicting tree cover across biophysical gradients, such as precipitation or agricultural cover. To generate a natural forest cover map for Costa Rica, biases in tree cover estimation in the most widely used tree cover product (the Global Forest Change product (GFC) were quantified and corrected, and the impact of map biases on estimates of forest cover and fragmentation was examined. First, a forest reference dataset was developed to examine how the difference between reference and GFC-predicted tree cover estimates varied along gradients of precipitation and elevation, and nonlinear statistical models were fit to predict the bias. Next, an agricultural land cover map was generated by classifying Landsat and ALOS PalSAR imagery (overall accuracy of 97%) to allow removing six common agricultural crops from estimates of tree cover. Finally, the GFC product was corrected through an integrated process using the nonlinear predictions of precipitation and elevation biases and the agricultural crop map as inputs. The accuracy of tree cover prediction increased by ≈29% over the original global forest change product (the R2 rose from 0.416 to 0.538). Using an optimized 89% tree cover threshold to create a forest/nonforest map, we found that fragmentation declined and core forest area and connectivity increased in the corrected forest cover map, especially in dry tropical forests, protected areas, and designated habitat corridors. By contrast, the core forest area decreased locally where agricultural fields were removed from estimates of natural tree cover. This research demonstrates a simple, transferable methodology to correct for observed biases in the Global Forest Change product. The use of uncorrected tree cover products may markedly over- or underestimate forest cover and fragmentation, especially in tropical regions with low precipitation, significant topography, and/or perennial agricultural production.

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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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One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

Genetics in Medicine ◽

10.1038/s41436-021-01187-w ◽

2021 ◽

Author(s):

Stephen E. Lincoln ◽

Tina Hambuch ◽

Justin M. Zook ◽

Sara L. Bristow ◽

Kathryn Hatchell ◽

...

Keyword(s):

Diagnostic Yield ◽

Copy Number Variants ◽

Low Complexity ◽

Clinical Genetic ◽

Clinical Sensitivity ◽

Pathogenic Variants ◽

Wide Range ◽

Large Indels ◽

Next Generation Sequencing Ngs ◽

The Impact

Abstract Purpose To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. Methods An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)–based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. Results In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. Conclusion The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.

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Evaluation of a Coupled Model to Predict the Impact of Adaptive Behaviour in the Thermal Sensation of Occupants of Naturally Ventilated Buildings in Warm-Humid Regions

Sustainability ◽

10.3390/su13010255 ◽

2020 ◽

Vol 13 (1) ◽

pp. 255

Author(s):

Luciano C. de Faria ◽

Marcelo A. Romero ◽

Lúcia F. S. Pirró

Keyword(s):

Computational Models ◽

Thermal Sensation ◽

Coupled Model ◽

Adaptive Behaviour ◽

Humid Climate ◽

Clothing Insulation ◽

Tropical Regions ◽

Naturally Ventilated Buildings ◽

Adaptive Behaviours ◽

The Impact

Improving indoor environment quality and making urban centres in tropical regions more sustainable has become a challenge for which computational models for the prediction of thermal sensation for naturally ventilated buildings (NVBs) have major role to play. This work performed analysis on thermal sensation for non-residential NVBs located in Brazilian tropical warm-humid climate and tested the effectiveness of suggested adaptive behaviours to mitigate warm thermal sensation. The research method utilized transient computational fluid dynamics models coupled with a dynamic model for human thermophysiology to predict thermal sensation. The calculated results were validated with comparison with benchmark values from questionnaires and from field measurements. The calculated results for dynamic thermal sensation (DTS) seven-point scale showed higher agreement with the thermal sensation vote than with the predicted mean vote. The test for the suggested adaptive behaviours considered reducing clothing insulation values from 0.18 to 0.32 clo (reducing DTS from 0.1 to 0.9), increasing the air speed in 0.9 m/s (reducing DTS from 0.1 to 0.9), and applying both suggestions together (reducing DTS from 0.1 to 1.3) for five scenarios with operative temperatures spanning 34.5–24.0 °C. Results quantified the tested adaptive behaviours’ efficiency showing applicability to improve thermal sensation from slightly-warm to neutral.

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The interaction of seasonal rainfall and nitrogen fertiliser rate on soil N2O emission, total N loss and crop yield of dryland sorghum and sunflower grown on sub-tropical Vertosols

Soil Research ◽

10.1071/sr15286 ◽

2016 ◽

Vol 54 (5) ◽

pp. 604 ◽

Cited By ~ 23

Author(s):

G. D. Schwenke ◽

B. M. Haigh

Keyword(s):

Crop Yield ◽

Crop Production ◽

Field Experiments ◽

N2o Emission ◽

N2o Emissions ◽

N Loss ◽

N Losses ◽

Total N ◽

Tropical Regions ◽

The Impact

Summer crop production on slow-draining Vertosols in a sub-tropical climate has the potential for large emissions of soil nitrous oxide (N2O) from denitrification of applied nitrogen (N) fertiliser. While it is well established that applying N fertiliser will increase N2O emissions above background levels, previous research in temperate climates has shown that increasing N fertiliser rates can increase N2O emissions linearly, exponentially or not at all. Little such data exists for summer cropping in sub-tropical regions. In four field experiments at two locations across two summers, we assessed the impact of increasing N fertiliser rate on both soil N2O emissions and crop yield of grain sorghum (Sorghum bicolor L.) or sunflower (Helianthus annuus L.) in Vertosols of sub-tropical Australia. Rates of N fertiliser, applied as urea at sowing, included a nil application, an optimum N rate and a double-optimum rate. Daily N2O fluxes ranged from –3.8 to 2734g N2O-Nha–1day–1 and cumulative N2O emissions ranged from 96 to 6659g N2O-Nha–1 during crop growth. Emissions of N2O increased with increased N fertiliser rates at all experimental sites, but the rate of N loss was five times greater in wetter-than-average seasons than in drier conditions. For two of the four experiments, periods of intense rainfall resulted in N2O emission factors (EF, percent of applied N emitted) in the range of 1.2–3.2%. In contrast, the EFs for the two drier experiments were 0.41–0.56% with no effect of N fertiliser rate. Additional 15N mini-plots aimed to determine whether N fertiliser rate affected total N lost from the soil–plant system between sowing and harvest. Total 15N unaccounted was in the range of 28–45% of applied N and was presumed to be emitted as N2O+N2. At the drier site, the ratio of N2 (estimated by difference)to N2O (measured) lost was a constant 43%, whereas the ratio declined from 29% to 12% with increased N fertiliser rate for the wetter experiment. Choosing an N fertiliser rate aimed at optimum crop production mitigates potentially high environmental (N2O) and agronomic (N2+N2O) gaseous N losses from over-application, particularly in seasons with high intensity rainfall occurring soon after fertiliser application.

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Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.0706 ◽

2012 ◽

Vol 279 (1742) ◽

pp. 3520-3526 ◽

Cited By ~ 37

Author(s):

Brian Tilston Smith ◽

Amei Amei ◽

John Klicka

Keyword(s):

Bird Species ◽

Tropical Regions ◽

Isthmus Of Panama ◽

Species Pairs ◽

The Matrix ◽

High Species Richness ◽

The Rich ◽

The Tropics ◽

The Impact

Climatic and geological changes across time are presumed to have shaped the rich biodiversity of tropical regions. However, the impact climatic drying and subsequent tropical rainforest contraction had on speciation has been controversial because of inconsistent palaeoecological and genetic data. Despite the strong interest in examining the role of climatic change on speciation in the Neotropics there has been few comparative studies, particularly, those that include non-rainforest taxa. We used bird species that inhabit humid or dry habitats that dispersed across the Panamanian Isthmus to characterize temporal and spatial patterns of speciation across this barrier. Here, we show that these two assemblages of birds exhibit temporally different speciation time patterns that supports multiple cycles of speciation. Evidence for these cycles is further corroborated by the finding that both assemblages consist of ‘young’ and ‘old’ species, despite dry habitat species pairs being geographically more distant than pairs of humid habitat species. The matrix of humid and dry habitats in the tropics not only allows for the maintenance of high species richness, but additionally this study suggests that these environments may have promoted speciation. We conclude that differentially expanding and contracting distributions of dry and humid habitats was probably an important contributor to speciation in the tropics.

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