scholarly journals Nitrogen release from five organic fertilizers commonly used in greenhouse organic horticulture with contrasting effects on bacterial communities

2020 ◽  
pp. 1-16 ◽  
Author(s):  
Pierre-Paul Dion ◽  
Thomas Jeanne ◽  
Mireille Thériault ◽  
Richard Hogue ◽  
Steeve Pepin ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Mineral Soil ◽  
Organic Fertilizers ◽  
Organic N ◽  
Rrna Gene ◽  
N Availability ◽  
Organic Fertilization ◽  
Growing Medium ◽  
Organic Horticulture ◽  
The Impact

Organic fertilization in greenhouses relies on organic fertilizers with low carbon/nitrogen ratio. Nitrogen (N) availability thus depends on an efficient mineralization driven by microbial communities. However, data on the mineralization rate of such fertilizers are scarce, and their improper use can lead to either N deficiency, or N losses to the environment. Consequently, better knowledge of N availability following organic fertilization is crucial for the development of sustainable greenhouse organic horticulture. We investigated the effect of pelleted poultry manure (PM) and blood (BM), feather (FM), alfalfa (AM), and shrimp (SM) meals on N availability and bacterial communities in a peat-based organic growing medium and a mineral soil. Nitrogen and carbon (C) pools were measured periodically over a 52 wk incubation experiment. Bacterial communities were characterized by sequencing the regions V6–V8 of the 16S rRNA gene on the high-throughput Illumina MiSeq platform, 4 wk after the start of the incubation. Nitrogen mineralization plateaued for the mineral soil and the peat substrate at, respectively, 41% and 63% of applied N for PM, 56%–93% (BM), 54%–81% (FM), 34%–53% (AM), and 57%–73% (SM). Organic fertilizers supported markedly contrasted bacterial communities, closely linked to soil biochemical properties, especially mineral N, pH, and soluble C. Alfalfa meal promoted the highest Shannon diversity index in the mineral soil, whereas SM and PM increased it in the peat-based growing medium. Our results quantified the mineralization and highlighted the impact on bacterial communities of commonly used organic N fertilizers in conditions relevant to organic greenhouse horticulture.

scholarly journals Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions

2021 ◽  
Author(s):  
A. Shore ◽  
R. D. Day ◽  
J. A. Stewart ◽  
C.A. Burge
Keyword(s):  
Ocean Acidification ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Ph Gradient ◽  
Rrna Gene ◽  
Seawater Ph ◽  
Coral Health ◽  
And Function ◽  
The Impact

Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Marianas Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. By contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean. IMPORTANCE Ocean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e. calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under mid-range IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.

scholarly journals The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

2021 ◽  
Author(s):  
Aitana Ares ◽  
Joana Pereira ◽  
Eva Garcia ◽  
Joana Costa ◽  
Igor Tiago
Keyword(s):  
Bacterial Community ◽  
Pseudomonas Syringae ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Defense Mechanisms ◽  
Abiotic Factors ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

scholarly journals Nitrogen Availability from High-nitrogen-containing Organic Fertilizers

2006 ◽  
Vol 16 (1) ◽  
pp. 39-42 ◽  
Author(s):  
T.K. Hartz ◽  
P.R. Johnstone
Keyword(s):  
Blood Meal ◽  
Nitrogen Availability ◽  
Organic Fertilizers ◽  
Organic N ◽  
N Availability ◽  
Vegetable Production ◽  
Feather Meal ◽  
Available N ◽  
Organic Vegetable Production ◽  
Seabird Guano

Limited soil nitrogen (N) availability is a common problem in organic vegetable production that often necessitates in-season fertilization. The rate of net nitrogen mineralization (Nmin) from four organic fertilizers (seabird guano, hydrolyzed fish powder, feather meal, and blood meal) containing between 11.7% and 15.8% N was compared in a laboratory incubation. The fertilizers were mixed with soil from a field under organic management and incubated aerobically at constant moisture at 10, 15, 20, and 25 °C. Nmin was determined on samples extracted after 1, 2, 4, and 8 weeks. Rapid Nmin was observed from all fertilizers at all temperatures; within 2 weeks between 47% and 60% of organic N had been mineralized. Temperature had only modest effects, with 8-week Nmin averaging 56% and 66% across fertilizers at 10 and 25 °C, respectively. Across temperatures, 8-week Nmin averaged 60%, 61%, 62%, and 66% for feather meal, seabird guano, fish powder, and blood meal, respectively. Cost per unit of available N (mineralized N + initial inorganic N) varied widely among fertilizers, with feather meal the least and fish powder the most expensive.

scholarly journals Nutrient Availability under Lettuce Grown in Rye Mulch in Histosols

Nitrogen ◽  
2020 ◽  
Vol 1 (2) ◽  
pp. 137-150
Author(s):  
Jacynthe Dessureault-Rompré ◽  
Alexis Gloutney ◽  
Jean Caron
Keyword(s):  
Nutrient Availability ◽  
Crop Production ◽  
Growing Season ◽  
Organic N ◽  
N Availability ◽  
Long Term Effects ◽  
Vegetable Crop ◽  
Conservation Practice ◽  
Lettuce Growth ◽  
The Impact

Vegetable crop production, which is expanding worldwide, is managed extremely intensively and is therefore raising concerns about soil degradation. The objective of this study was to analyze the impact of using rye mulch as a conservation practice on nutrient availability for lettuce grown in histosols. The rye cover crop was established in the fall of 2018 at two cultivated peatland sites. The following summer, lettuce crops were planted at both sites on the rye mulch cover and on control plots. Lysimeters were used to extract the soil solution once a week during lettuce growth. Various soil properties were analyzed in the soil sampled at the end of the lettuce growing season. The rye yield was higher at site 1 than at site 2 and the lettuce growth was reduced at site 1 under the rye mulch treatment. The rye mulch reduced mineral N and dissolved organic N availability at both sites. The N dynamics in histosols might be fast enough to supply the lettuce needs; however, the implantation difficulties must first be overcome to confirm that hypothesis. At the end of the lettuce growth period, soil total and active C pools and soluble organic soil N in the rye mulch treatment sample were significantly higher at site 1 than at site 2. The presence of rye mulch improved the carbon pool over a single growing season. The use of rye mulch as a soil conservation practice for vegetable crop production appears promising for histosols; however, more work is needed to gain a better understanding on the long-term effects of decomposing rye mulch and roots on soil nutrient availability, soil health and C sequestration, and on the nitrogen uptake pathways and growth of cash crops. Future works which would include consecutive years of study at multiple sites are also needed to be able to confirm and generalize the observations found in the present work.

scholarly journals Pakchoi Antioxidant Improvement and Differential Rhizobacterial Community Composition under Organic Fertilization

2019 ◽  
Vol 11 (8) ◽  
pp. 2424
Author(s):  
Jianli Liao ◽  
Jun Ye ◽  
Yun Liang ◽  
Muhammad Khalid ◽  
Danfeng Huang
Keyword(s):  
Community Structure ◽  
Plant Biomass ◽  
Inorganic Nitrogen ◽  
Organic Fertilizer ◽  
Chemical Fertilizer ◽  
Organic Fertilizers ◽  
Organic N ◽  
Soil Conditions ◽  
Fertilizer Treatment ◽  
Organic Fertilization

A high level of antioxidants in organic-produced vegetables has been attributed to soil conditions; however, little is known about the relationships between antioxidants and rhizobacteria under different fertilization treatments. A pot trial for pakchoi (Brassica campestris ssp. chinensis L.) was conducted under greenhouse conditions with: (1) control; (2) chemical fertilizer; and (3) organic fertilizer. The responses of the plant, soil properties, and rhizobacterial community were measured after 45 days of cultivation. Fertilization increased soil nutrient levels and pakchoi productivity and the reshaped rhizobacterial community structure, while no differences in rhizobacterial abundance and total diversity were observed. Generally, most plant antioxidants were negatively correlated with inorganic nitrogen (N) and positively correlated to organic N in soil. The genera of Arthrospira and Acutodesmus contained differential rhizobacteria under chemical fertilizer treatment, which are known as copiotrophs. In addition, the addition of a chemical fertilizer may stimulate organic substance turnover by the enrichment of organic compound degraders (e.g., Microbacterium and Chitinophaga) and the promotion of predicted functional pathways involved in energy metabolism. Several beneficial rhizobacteria were associated with organic fertilizer amended rhizosphere including the genera Bacillus, Mycobacterium, Actinomycetospora, and Frankia. Furthermore, Bacillus spp. were positively correlated with plant biomass and phenolic acid. Moreover, predictive functional profiles of the rhizobacterial community involved in amino acid metabolism and lipid metabolism were significantly increased under organic fertilization, which were positively correlated with plant antioxidant activity. Overall, our study suggests that the short-term application of chemical and organic fertilizers reshapes the rhizobacterial community structure, and such changes might contribute to the plant’s performance.

scholarly journals Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

2004 ◽  
Vol 70 (2) ◽  
pp. 804-813 ◽  
Author(s):  
Christian Winter ◽  
Arjan Smit ◽  
Gerhard J. Herndl ◽  
Markus G. Weinbauer
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Tropical Atlantic ◽  
Viral Lysis ◽  
Batch Cultures ◽  
Operational Taxonomic Units ◽  
The Impact

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

scholarly journals Marine cyanolichens from different littoral zones are associated with distinct bacterial communities

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5208 ◽  
Author(s):  
Nyree J. West ◽  
Delphine Parrot ◽  
Claire Fayet ◽  
Martin Grube ◽  
Sophie Tomasi ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Littoral Zone ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Moderately Thermophilic ◽  
Culture Independent ◽  
Radiation Resistant ◽  
Bacteroidetes Phylum ◽  
And Function ◽  
The Impact

The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen speciesLichina pygmaeaandLichina confinis, and the maritime chlorolichen speciesXanthoria aureolawhich occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. TheL. confinisandL. pygmaeacommunities were significantly different from those of the maritimeXanthoria aureolalichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notablySphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the twoLichinaspecies were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes generaRubricoccus,TunicatimonasandLewinella, suggesting an important role of these species in the marineLichinalichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.

scholarly journals On a Reef Far, Far Away: Anthropogenic Impacts Following Extreme Storms Affect Sponge Health and Bacterial Communities

2021 ◽  
Vol 8 ◽  
Author(s):  
Amanda Shore ◽  
Jordan A. Sims ◽  
Michael Grimes ◽  
Lauren I. Howe-Kerr ◽  
Carsten G. B. Grupstra ◽  
...  
Keyword(s):  
Climate Change ◽  
Bacterial Communities ◽  
Anthropogenic Impacts ◽  
Global Climate ◽  
Climate Change Impacts ◽  
Rrna Gene ◽  
Benthic Organisms ◽  
Severe Storms ◽  
The Impact ◽  
Offshore Reef

Terrestrial runoff can negatively impact marine ecosystems through stressors including excess nutrients, freshwater, sediments, and contaminants. Severe storms, which are increasing with global climate change, generate massive inputs of runoff over short timescales (hours to days); such runoff impacted offshore reefs in the northwest Gulf of Mexico (NW GoM) following severe storms in 2016 and 2017. Several weeks after coastal flooding from these events, NW GoM reef corals, sponges, and other benthic invertebrates ∼185 km offshore experienced mortality (2016 only) and/or sub-lethal stress (both years). To assess the impact of storm-derived runoff on reef filter feeders, we characterized the bacterial communities of two sponges, Agelas clathrodes and Xestospongia muta, from offshore reefs during periods of sub-lethal stress and no stress over a three-year period (2016—2018). Sponge-associated and seawater-associated bacterial communities were altered during both flood years. Additionally, we found evidence of wastewater contamination (based on 16S rRNA gene libraries and quantitative PCR) in offshore sponge samples, but not in seawater samples, following these flood years. Signs of wastewater contamination were absent during the no-flood year. We show that flood events from severe storms have the capacity to reach offshore reef ecosystems and impact resident benthic organisms. Such impacts are most readily detected if baseline data on organismal physiology and associated microbiome composition are available. This highlights the need for molecular and microbial time series of benthic organisms in near- and offshore reef ecosystems, and the continued mitigation of stormwater runoff and climate change impacts.

scholarly journals Groundwater bacterial communities evolve over time, exhibiting oscillating similarity patterns in response to recharge

2021 ◽  
Author(s):  
Lijuan Yan ◽  
Syrie Hermans ◽  
Kai Uwe Totsche ◽  
Robert Lehmann ◽  
Martina Herrmann ◽  
...  
Keyword(s):  
Groundwater Recharge ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
High Temporal Resolution ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Environmental Selection ◽  
The Impact ◽  
Over Time

Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in groundwater bacterial communities of shallow fractured bedrock community, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n=230) along a hillslope recharge area. We show that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and showed oscillating dissimilarity patterns which corresponded to periods of groundwater recharge; the impact of recharge events on the groundwater microbiome was linked to the recharge strength and local environmental selection strength. Sampling period was able to explain up to 29.5% of the variability in bacterial community composition. We observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The majority of groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, groundwater microbiomes vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the complex dynamics of bacterial communities in groundwater and demonstrated that successive shocks disturb the bacterial communities, leading to decreased similarity to the initial state over time.

scholarly journals Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. Chemidlin Prévost-Bouré ◽  
B. Karimi ◽  
S. Sadet-Bourgeteau ◽  
C. Djemiel ◽  
M. Brie ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Dairy Farms ◽  
Raw Milk ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Farming Practices ◽  
Organic Fertilization ◽  
Grassland Ecosystems ◽  
Protected Designation Of Origin

AbstractThe specificity of dairy Protected Designation of Origin (PDO) products is related to their “terroir” of production. This relationship needs better understanding for efficient and sustainable productions preserving the agroecological equilibrium of agroecosystems, especially grasslands. Specificity of PDO Comté cheese was related to the diversity of natural raw milk bacterial communities, but their sources need to be determined. It is hypothesized that raw milk indigenous microbial communities may originate from permanent grazed grasslands by the intermediate of dairy cows according to the sequence soil–phyllosphere–teat–milk. This hypothesis was evaluated on a 44 dairy farms network across PDO Comté cheese area by characterizing prokaryotic and fungal communities of these compartments by metabarcoding analysis (16S rRNA gene: V3–V4 region, 18S rRNA gene: V7–V8 region). Strong and significant links were highlighted between the four compartments through a network analysis (0.34 < r < 0.58), and were modulated by soil pH, plant diversity and elevation; but also by farming practices: organic fertilization levels, cattle intensity and cow-teat care. This causal relationship suggests that microbial diversity of agroecosystems is a key player in relating a PDO product to its “terroir”; this under the dependency of farming practices. Altogether, this makes the “terroir” even more local and needs to be considered for production sustainability.

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