scholarly journals Filtered mud improves sugarcane growth and modifies the functional abundance and structure of soil microbial populations

PeerJ ◽  
2022 ◽  
Vol 10 ◽  
pp. e12753
Author(s):  
Ahmad Yusuf Abubakar ◽  
Muhammed Mustapha Ibrahim ◽  
Caifang Zhang ◽  
Muhammad Tayyab ◽  
Nyumah Fallah ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Soil Nutrient ◽  
Clay Loam ◽  
Sugarcane Production ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Soil Nutrient Cycling ◽  
Growth Properties

Background Exploring high-quality organic amendments has been a focus of sustainable agriculture. Filtered mud (FM), a sugar factory waste derived from sugarcane stems, could be an alternative organic amendment for sugarcane production. However, the effects of its application proportions on soil fertility, nutrient cycling, structure of soil bacterial and fungal communities, and the growth of sugarcane in clay-loam soils remain unexplored. Methods Three application proportions of FM: (FM1-(FM: Soil at 1:4), FM2-(FM: Soil at 2:3), and FM3-(FM: Soil at 3:2)) were evaluated on sugarcane growth and soil nutrient cycling. High throughput sequencing was also employed to explore soil microbial dynamics. Results We observed that FM generally increased the soil’s nutritional properties while improving NO3− retention compared to the control, resulting in increased growth parameters of sugarcane. Specifically, FM1 increased the concentration of NH4+−N, the N fraction preferably taken up by sugarcane, which was associated with an increase in the plant height, and more improved growth properties, among other treatments. An increase in the proportion of FM also increased the activity of soil nutrient cycling enzymes; urease, phosphatase, and β-glucosidase. High throughput sequencing revealed that FM reduced the diversity of soil bacteria while having insignificant effects on fungal diversity. Although increasing FM rates reduced the relative abundance of the phyla Proteobacteria, its class members, the Gammaproteobacteria and Betaproteobacteria containing some N-cycling related genera, were stimulated. Also, FM stimulated the abundance of beneficial and lignocellulose degrading organisms. These included the bacterial phyla Actinobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and the fungal phylum Ascomycota. The distribution of the soil microbial community under FM rates was regulated by the changes in soil pH and the availability of soil nutrients. Since FM1 showed more promise in improving the growth properties of sugarcane, it could be more economical and sustainable for sugarcane production in clay-loam soils.

scholarly journals Association of biochar properties with changes in soil bacterial, fungal and fauna communities and nutrient cycling processes

Biochar ◽  
2021 ◽  
Author(s):  
Zhongmin Dai ◽  
Xinquan Xiong ◽  
Hang Zhu ◽  
Haojie Xu ◽  
Peng Leng ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Soil Nutrient ◽  
Growth Promoters ◽  
Soil Microbial ◽  
Soil Nutrient Cycling ◽  
Microbial Responses ◽  
Underlying Mechanisms ◽  
Microbial Groups ◽  
N And P Cycling ◽  
Crop Health

AbstractSoil microorganisms play crucial roles in soil nutrient cycling, carbon sequestration, fertility maintenance and crop health and production. To date, the responses of microorganisms, such as microbial activity, diversity, community structure and nutrient cycling processes, to biochar addition have been widely reported. However, the relationships between soil microbial groups (bacteria, fungi and microscopic fauna) and biochar physicochemical properties have not been summarized. In this review, we conclude that biochar affects soil microbial growth, diversity and community compositions by directly providing growth promoters for soil biota or indirectly changing soil basic properties. The porous structure, labile C, high pH and electrochemical properties of biochar play an important role in determining soil microbial abundance and communities, and their mediated N and P cycling processes, while the effects and underlying mechanisms vary with biochar types that are affected by pyrolysis temperature and feedstock type. Finally, we highlight some issues related to research methodology and subjects that are still poorly understood or controversial, and the perspectives for further research in microbial responses to biochar addition.

scholarly journals Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Shuo Jiao ◽  
Ziheng Peng ◽  
Jiejun Qi ◽  
Jiamin Gao ◽  
Gehong Wei
Keyword(s):  
Nutrient Cycling ◽  
Microbial Diversity ◽  
Soil Nutrient ◽  
Terrestrial Ecosystems ◽  
Ecosystem Functions ◽  
Soil Biodiversity ◽  
Soil Microbial ◽  
Soil Nutrient Cycling ◽  
Potential Factors ◽  
Fungal Associations

ABSTRACT Biodiversity is important for supporting ecosystem functioning. To evaluate the factors contributing to the strength of microbial diversity-function relationships in complex terrestrial ecosystems, we conducted a soil survey over different habitats, including an agricultural field, forest, wetland, grassland, and desert. Soil microbial multidiversity was estimated by the combination of bacterial and fungal diversity. Soil ecosystem functions were evaluated using a multinutrient cycling index (MNC) in relation to carbon, nitrate, phosphorus, and potassium cycling. Significant positive relationships between soil multidiversity and multinutrient cycling were observed in all habitats, except the grassland and desert. Specifically, community compositions showed stronger correlations with multinutrient cycling than α-diversity, indicating the crucial role of microbial community composition differences on soil nutrient cycling. Importantly, we revealed that changes in both the neutral processes (Sloan neutral modeling) and the proportion of negative bacterial-fungal associations were linked to the magnitude and direction of the diversity-MNC relationships. The habitats less governed by neutral processes and dominated by negative bacterial-fungal associations exhibited stronger negative microbial α-diversity–MNC relationships. Our findings suggested that the balance between positive and negative bacterial-fungal associations was connected to the link between soil biodiversity and ecosystem function in complex terrestrial ecosystems. This study elucidates the potential factors influencing diversity-function relationships, thereby enabling future studies to forecast the effects of belowground biodiversity on ecosystem function. IMPORTANCE The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. Our structural equation modeling and random forest analysis revealed that the balance between positive and negative bacterial-fungal associations was clearly linked to the strength of the relationships between soil microbial diversity and multiple nutrients cycling across different habitats. This study revealed the potential factors underpinning diversity-function relationships in terrestrial ecosystems and thus helps us to manage soil microbial communities for better provisioning of key ecosystem services.

scholarly journals Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

2020 ◽  
Author(s):  
Jane Oja ◽  
Sakeenah Adenan ◽  
Abdel-Fattah Talaat ◽  
Juha Alatalo
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Arbuscular Mycorrhizal ◽  
Soil Microbial ◽  
Fungal Abundance ◽  
Novel Approach ◽  
Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

scholarly journals High-Throughput, Sequence-Based Analysis of the Microbiota of Greek Kefir Grains from Two Geographic Regions

2020 ◽  
Vol 58 (2) ◽  
pp. 138-146
Author(s):  
Mary S. Kalamaki ◽  
Apostolos S. Angelidis
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Geographic Origin ◽  
Probiotic Properties ◽  
Sequencing Analysis ◽  
Microbial Composition ◽  
Bacterial Phyla ◽  
Geographic Regions ◽  
Kefir Grains

Research background. Kefir is a natural probiotic drink traditionally produced by milk fermentation using kefir grains. Kefir grains are composed of a complex population of bacteria and yeasts embedded in a polysaccharide-protein matrix. The geographic origin of kefir grains may largely influence their microbial composition and the associated kefir drink properties. Although the detailed bacterial composition of kefir grains from several geographic regions has been reported, to date, analogous data about the microbiome of Greek kefir are lacking. Hence, the aim of this study is to investigate the structure and the diversity of the bacterial community of Greek kefir grains.Experimental approach. The bacterial community structure and diversity of two different kefir grains from distant geographic regions in Greece were examined via high-throughput sequencing analysis, a culture-independent metagenomic approach, targeting the 16S rRNA V4 variable region, in order to gain a deeper understanding of their bacterial population diversities.Results and conclusions. Firmicutes (a phylum that includes lactic acid bacteria) was strikingly dominant amongst the identified bacterial phyla, with over 99 % of the sequences from both kefir grains classified to this phylum. At the family level, Lactobacillaceae sequences accounted for more than 98 % of the operational taxonomic units (OTUs), followed by Ruminococcaceae, Lahnospiraceae, Bacteroidaceae and other bacterial families of lesser abundance. Α relatively small number of bacterial genera dominated, with Lactobacillus kefiranofaciens being the most abundant in both kefir grains (95.0 % of OTUs in kefir A and 96.3 % of OTUs in kefir B). However, a quite variable subdominant population was also present in both grains, including bacterial genera that have been previously associated with the gastrointestinal tract of humans and animals, some of which are believed to possess probiotic properties (Faecalibacterium spp., Bacteroides spp., Blautia spp.). Differences among the bacterial profiles of the two grains were very small indicating a high homogeneity despite the distant geographic origin.Novelty and scientific contribution. This is the first study to deeply explore and report on the bacterial diversity and species richness of Greek kefir.

Effect of Drought and Recovery on Grazing Animal, Microbial, and Fungal Response in a Diverse Multi-Crop Rotation

2020 ◽  
Author(s):  
Douglas Landblom ◽  
Songul Senturklu
Keyword(s):  
Nutrient Cycling ◽  
Beef Cattle ◽  
Microbial Activity ◽  
Crop Rotation ◽  
Cover Crop ◽  
Crop Production ◽  
Microbial Respiration ◽  
Soil Nutrient ◽  
Soil Microbial ◽  
Animal Grazing

<p>Beef cattle grazing, soil microbial respiration, and Rhizobia spp. populations serve important roles in soil nutrient cycling and during periods of drought, when abnormal precipitation declines, forage production for animal grazing and performance are negatively impacted. Soil nutrient availability is essential for adequate crop production and extended drought reduces soil microbial activity and therefore nutrient cycling. During the 2017 growing season between April and October in the northern Great Plains region of the USA, effective precipitation for crop production and animal grazing was severely reduced due an exceptional drought as classified by the US Drought Monitor. At the NDSU – Dickinson Research Extension Center, Dickinson, North Dakota, USA, a long-term integrated system that includes yearling steer grazing within a diverse multi-crop rotation (spring wheat, cover crop, corn, pea-barley intercrop, and sunflower). Within the rotation of cash and forage crops, beef cattle graze the pea-barley, corn, and cover crop (13-specie) within the rotation and is being utilized to monitor the effects of animal, microbial and fungal activity over time and space in the crop and animal production system. Nitrogen fertilizer has been replaced in the system by soil microbial and fungal activity (Potential Mineralizable Nitrogen: 8.4 mg N/kg) such that for each 1% increase in SOM there is a corresponding increase of 18.8 kg of potential nitrogen mineralized per ha. Animal grazing days are severely reduced when precipitation is inadequate for soil microbial respiration to occur. What is even more concerning, when relying on microbial activity to supply plant nutrients, is recovery time for microbial activity to fully recover from exceptional drought as was the case in this research project. Compared to the 2016 crop production year that preceded the 2017 drought, cover crop (13-specie), pea-barley, and corn yields were reduced 86, 33, and 64% during the 2017 drought. This decline in crop production reduced the number of days of grazing by an average 50% and average daily gains were also reduced. Steer average daily gains were 1.05 0.95, and 0.83 kg/steer/day in 2017 when grazing pea-barley, corn, and cover crop, respectively. For this research that relies on soil derived plant nutrients soil analysis for microbial and Rhizobia spp. biomass began recovery in 2018 and continued into 2019 as evidenced by large percentage increases in organism biomass; however, complete production recovery did not occur by the end of the 2019 grazing season in which days of grazing were reduced compared to the 2016 grazing season. Biological animal, crop, microbial, fungal, and nutrient replacement recovery will be presented in the poster.</p>

Interactions between plant growth and soil nutrient cycling under elevated CO2 : a meta-analysis

2006 ◽  
Vol 12 (11) ◽  
pp. 2077-2091 ◽  
Author(s):  
MARIE-ANNE De GRAAFF ◽  
KEES-JAN Van GROENIGEN ◽  
JOHAN SIX ◽  
BRUCE HUNGATE ◽  
CHRIS Van KESSEL
Keyword(s):  
Plant Growth ◽  
Nutrient Cycling ◽  
Elevated Co2 ◽  
Meta Analysis ◽  
Soil Nutrient ◽  
Soil Nutrient Cycling

scholarly journals Identification of Drug Targets and Potential Molecular Mechanisms of Wantong Jingu Tablet in Treatment of Rats with Collagen-Induced Arthritis based on 16S rDNA High-Throughput Sequencing and Metabolomic Analysis

2020 ◽  
Author(s):  
Zhaodong Li ◽  
Fangyuan Qi ◽  
Fan Li
Keyword(s):  
16S Rdna ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Caspase 3 ◽  
Collagen Induced Arthritis ◽  
Apoptosis Pathway ◽  
Bacterial Phyla ◽  
Joint Pathology

Abstract Background: Wantong Jingu Tablet (WJT), a mixture of traditional Chinese medicine, can reduce the symptoms of rheumatoid arthritis (RA), but its pharmacological mechanism is unclear. The aims of this study were to investigate the therapeutic mechanisms of WJT for RA in vivo.Methods: The effects of WJT on the joint pathology, and the levels of Bax, Bcl-2,caspase-3, cleaved-caspase-3, ERK1/2, pERK1/2, TNF-α, IL-1β, and IL-6 were demonstrated based on several experiments in the model of collagen-induced arthritis (CIA) in rats. 16S rDNA high-throughput sequencing was used to investigate the effect of WJT on the overall structure and composition of gut microbiota. Meanwhile, metabolite changes in faeces were analyzed by metabolomics techniques. Results: The results showed that WJT restored the joint pathology in CIA rats, upregulated Bax and cleaved-caspase-3, downregulated Bcl-2, caspase-3, and pERK1/2, and reduced the levels of pro-inflammatory cytokines. The overall gut microbial structure in CIA rats was altered after WJT treatment. Three bacterial phyla were prominently restored: Bacteroidetes,Tenericutes and Deferribacteres, and three bacterial genera were significantly reversed: Vibrio, Macrococcus and Vagococcus. Furthermore, five specific metabolites associated with these specific bacterial genera were identified by correlation analysis. In addition, WJT supplement trended to down-regulate the other five metabolites according to metabolomic analyses. Conclusions: These results revealed that WJT restored the pathological changes of RA might through activating the mitochondrial apoptosis pathway, inhibited MEK/ERK signaling, and modulating the special bacteria and the special metabolites.

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