Erratum to: Soil Fertility and the Impact of Exotic Invasion on Microbial Communities in Hawaiian Forests

Abstract To exploit the potential of ecological intensification during sunflower cropping, it is crucial to understand the potential synergies between crop management and ecosystem services. We therefore examined the effect of pollination intensification on sunflower yield and productivity under various levels of soil fertilization over two seasons in the eastern Free State, South Africa. We manipulated soil fertility with fertilizer applications and pollination with exclusion bags. We found a synergetic effect between pollination and soil fertilization whereby increasing pollination intensity led to a far higher impact on sunflower yield when the soil had been fertilized. Specifically, the intensification of insect pollination increased seed yield by approximately 0.4 ton/ha on nutrient poor soil and by approximately 1.7 ton/ha on moderately fertilized soil. Our findings suggest that sunflower crops on adequate balanced soil fertility will receive abundant insect pollination and may gain more from both synergies than crops grown in areas with degraded soil fertility.

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Effect of Organic Amendment Addition on Soil Properties, Greenhouse Gas Emissions and Grape Yield in Semi-Arid Vineyard Agroecosystems

Agronomy ◽

10.3390/agronomy11081477 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1477

Author(s):

Antonio Marín-Martínez ◽

Alberto Sanz-Cobeña ◽

Mª Angeles Bustamante ◽

Enrique Agulló ◽

Concepción Paredes

Keyword(s):

Soil Fertility ◽

Soil Properties ◽

Greenhouse Gas ◽

Co2 Emissions ◽

Organic Amendments ◽

Organic N ◽

N2o Emissions ◽

The Impact ◽

Semi Arid ◽

Grape Yield

In semi-arid vineyard agroecosystems, highly vulnerable in the context of climate change, the soil organic matter (OM) content is crucial to the improvement of soil fertility and grape productivity. The impact of OM, from compost and animal manure, on soil properties (e.g., pH, oxidisable organic C, organic N, NH4+-N and NO3−-N), grape yield and direct greenhouse gas (GHG) emission in vineyards was assessed. For this purpose, two wine grape varieties were chosen and managed differently: with a rain-fed non-trellising vineyard of Monastrell, a drip-irrigated trellising vineyard of Monastrell and a drip-irrigated trellising vineyard of Cabernet Sauvignon. The studied fertiliser treatments were without organic amendments (C), sheep/goat manure (SGM) and distillery organic waste compost (DC). The SGM and DC treatments were applied at a rate of 4600 kg ha−1 (fresh weight, FW) and 5000 kg ha−1 FW, respectively. The use of organic amendments improved soil fertility and grape yield, especially in the drip-irrigated trellising vineyards. Increased CO2 emissions were coincident with higher grape yields and manure application (maximum CO2 emissions = 1518 mg C-CO2 m−2 d−1). In contrast, N2O emissions, mainly produced through nitrification, were decreased in the plots showing higher grape production (minimum N2O emissions = −0.090 mg N2O-N m−2 d−1). In all plots, the CH4 fluxes were negative during most of the experiment (−1.073−0.403 mg CH4-C m−2 d−1), indicating that these ecosystems can represent a significant sink for atmospheric CH4. According to our results, the optimal vineyard management, considering soil properties, yield and GHG mitigation together, was the use of compost in a drip-irrigated trellising vineyard with the grape variety Monastrell.

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Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

Nature Communications ◽

10.1038/s41467-021-23821-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Verónica Lloréns-Rico ◽

Sara Vieira-Silva ◽

Pedro J. Gonçalves ◽

Gwen Falony ◽

Jeroen Raes

Keyword(s):

Microbial Communities ◽

Quantitative Methods ◽

Microbial Load ◽

Metagenomic Sequencing ◽

Sampling Depth ◽

Microbiome Research ◽

Microbiome Data ◽

The Impact ◽

Analytical Approaches ◽

Quantitative Approaches

AbstractWhile metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.

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Microbial drivers of methane emissions from unrestored industrial salt ponds

The ISME Journal ◽

10.1038/s41396-021-01067-w ◽

2021 ◽

Author(s):

Jinglie Zhou ◽

Susanna M. Theroux ◽

Clifton P. Bueno de Mesquita ◽

Wyatt H. Hartman ◽

Ye Tian ◽

...

Keyword(s):

Microbial Communities ◽

Methane Flux ◽

Methane Emissions ◽

Metagenomic Data ◽

Rrna Gene ◽

Salt Ponds ◽

Salt Pond ◽

Reference Wetlands ◽

Reference Wetland ◽

The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

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The impact of various ozone pretreatment doses on the performance of endogenous microbial communities for the remediation of oil sands process-affected water

International Biodeterioration & Biodegradation ◽

10.1016/j.ibiod.2015.01.014 ◽

2015 ◽

Vol 100 ◽

pp. 17-28 ◽

Cited By ~ 25

Author(s):

Tao Dong ◽

Yanyan Zhang ◽

Md. Shahinoor Islam ◽

Yang Liu ◽

Mohamed Gamal El-Din

Keyword(s):

Microbial Communities ◽

Oil Sands ◽

Ozone Pretreatment ◽

The Impact

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The impact of nanoscale zero-valent iron particles on soil microbial communities is soil dependent

Journal of Hazardous Materials ◽

10.1016/j.jhazmat.2018.10.034 ◽

2019 ◽

Vol 364 ◽

pp. 591-599 ◽

Cited By ~ 11

Author(s):

María T. Gómez-Sagasti ◽

Lur Epelde ◽

Mikel Anza ◽

Julen Urra ◽

Itziar Alkorta ◽

...

Keyword(s):

Microbial Communities ◽

Soil Microbial Communities ◽

Zero Valent Iron ◽

Iron Particles ◽

Soil Microbial ◽

Nanoscale Zero Valent Iron ◽

The Impact

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Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

10.7287/peerj.preprints.3073 ◽

2017 ◽

Author(s):

Taha Soliman ◽

Sung-Yin Yang ◽

Tomoko Yamazaki ◽

Holger Jenke-Kodama

Keyword(s):

Next Generation Sequencing ◽

Microbial Communities ◽

Dna Extraction ◽

Dna Isolation ◽

Soil Microbial Communities ◽

Next Generation ◽

Microbial Composition ◽

Okinawa Island ◽

The Impact ◽

Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

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Nitrogen availability modulates the host control of the barley rhizosphere microbiota

10.1101/605204 ◽

2019 ◽

Cited By ~ 1

Author(s):

Rodrigo Alegria Terrazas ◽

Senga Robertson-Albertyn ◽

Aileen Mary Corral ◽

Carmen Escudero-Martinez ◽

Katharin Balbirnie-Cumming ◽

...

Keyword(s):

Plant Growth ◽

Microbial Communities ◽

Biological Processes ◽

N Application ◽

Plant Soil ◽

Unplanted Soil ◽

Bacterial Microbiota ◽

Soil Feedback ◽

The Impact ◽

Barley Genotypes

AbstractBackgroundSince the dawn of agriculture, human selection on plants has progressively differentiated input-demanding productive crops from their wild progenitors thriving in marginal areas. Barley (Hordeum vulgare), the fourth most cultivated cereal globally, is a prime example of this process. We previously demonstrated that wild and domesticated barley genotypes host distinct microbial communities in their rhizosphere. Here, we tested the hypothesis that microbiota diversification is modulated by, and responds to, nitrogen (N) application in soil and assessed the impact of microbiota taxonomic and functional compositions on plant growth.MethodsWe grew two wild (H. vulgare ssp. spontaneum) and an ‘Elite’ domesticated (H. vulgare ssp. vulgare) barley genotypes in an agricultural soil treated with and without N inputs. By using a two-pronged 16S rRNA gene amplicon sequencing and comparative metagenomics approach, we determined the impact of N application on taxonomic composition and metabolic potential of the microbial communities exposed to limiting and replete N supplies. We then implemented a plant-soil feedback experiment to assess microbiotas’ recruitment cues and contribution to plant growth.ResultsN availability emerged as a modulator of the recruitment cues of the barley bacterial microbiota as evidenced by the increased number of bacterial genera differentially recruited between unplanted soil and rhizosphere communities under N-limiting conditions. This recruitment pattern mirrored the impact of the host genotype on rhizosphere bacteria. The characterisation of the assembled metagenomes of plants exposed to N-limiting conditions revealed a metabolic specialisation of the rhizosphere microbiota compared to unplanted soil controls. This specialisation is underpinned predominantly by bacteria and is manifested by the enrichment of a core set of biological processes sustaining the adaptation of polymicrobial communities such as N utilisation, quorum sensing and motility across genotypes. The quantitative variation in a group of these biological processes defined host signatures in the barley rhizosphere metagenome. Finally, a plant-soil feedback experiment revealed that the host-mediated taxonomic diversification of the bacterial microbiota is associated with barley growth under sub-optimal N supplies.ConclusionsOur results suggest that under N limiting conditions, a substrate-driven selection process underpins the assembly of barley rhizosphere microbiota. Host-microbe and microbe-microbe interactions fine-tune this process at the taxonomic and functional level across kingdoms. The disruption of these recruitment cues negatively impacts plant growth.

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Effectiveness of Community-Based Soil and Water Conservation in Improving Soil Property in Damota Area, Southern Ethiopia

Applied and Environmental Soil Science ◽

10.1155/2021/5510587 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Mamush Masha ◽

Teshome Yirgu ◽

Mulugeta Debele ◽

Mengie Belayneh

Keyword(s):

Soil Fertility ◽

Water Conservation ◽

Agricultural Land ◽

Agricultural Landscapes ◽

Soil And Water Conservation ◽

Southern Ethiopia ◽

Conservation Practices ◽

Community Based ◽

The Impact ◽

Soil And Water

Soil and water conservation (SWC) is being advocated as an integral part of agricultural land management as it not only controls/minimizes soil erosion but also restores/rehabilitates the degraded lands. The purpose of this study was to evaluate the impact of soil and water conservation practices in improving soil fertility in the agricultural landscapes of the Damota area, southern Ethiopia. Forty-eight soil samples (both disturbed and core samples) were collected from the conserved and adjacent nonconserved plots. The significance analysis test was performed using analysis of variance. The result of the study showed that higher mean values of soil physicochemical properties were observed in the conserved plot than its nonconserved counterpart. The mean differences of organic carbon, total nitrogen, cation exchange capacity, and exchangeable K+ and Ca2+ between conserved and nonconserved plots were statistically significant at the P < 0.01 level. Besides, available phosphorous and bulk density were significant at P < 0.05 , but the effect of SWC practices was not found significant on soil texture, soil pH, and exchangeable Na+ and Mg2+ content of the soil in the Damota area. Community-based soil and water conservation practices have improved the soil fertility in agricultural landscapes, although significant results have been observed in some fertility indicators. Therefore, strengthening the implementation of conservation measures by participating in all stakeholders is recommended. Supporting physical structures by agronomic and vegetative measures and continued maintenance can bring better results.

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