ARTICLE | doi:10.20944/preprints202111.0076.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Weed science; Plant-microbe interactions; Medicinal plants; shotgun metagenomics; soil metabarcoding
Online: 3 November 2021 (09:19:12 CET)
The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Datura inoxia. We hypothesized that rhizospheric and endophytic microbes would be found that were capable of performing the same secondary metabolic functions of the plant rootzone they inhabited. We also hypothesized that the microbial functions would be co-operative with and supportive to plant secondary metabolite production, for example, by providing precursors to important plant bioactive molecules. The methods employed were mi-crobial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional. A few of the main bacterial genera of interest that were dis-covered in the Datura root microbiome were Flavobacterium, Chitinophaga, Pseudomonas, Strepto-myces, Rhizobium, and Bacillus. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. There was strong evidence to support the notion that synergistic production of plant de-rived secondary metabolites by microbes occurred, as well as the ability for the compounds to enter plant cells. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.
ARTICLE | doi:10.20944/preprints202211.0036.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Streptomyces; vegetable production; biofertilizer
Online: 2 November 2022 (02:59:42 CET)
A replicated outdoor pot experiment was conducted in order to investigate the effect of different phytohormone and siderophore producing, and P-solubilizing bacterial species on spinach nu-trient uptake, nitrate concentration and nitrate reductase activity. The mentioned parameters were determined in spinach leaves (Spinacia oleracea L.), non-inoculated and inoculated with four plant growth–promoting actinobacteria (Streptomyces griseus (S1), Streptomyces albogriseolus (S2), Strep-tomyces aurantiacus (S3) and Streptomyces kanamyceticus (S4) under the influence of two sources of nitrogen fertilizers including potassium nitrate and urea (100 and 200 ppm). Inoculation with the strains increased spinach shoot fresh weight by 16%–43% over the control. Bacterial inoculation gave leaf chlorophyll increases of 15%–40%. Inoculation increased plant height by 2.2%–24.6% in spinach. A close reverse relationship between nitrate concentration and enzyme activity (r2= 0.87) was demonstrated. The measured parameter responses were variable and dependent on the in-oculant strain, with highest enzyme activity and lowest nitrate concentration exhibited in S2 (S. albogriseolus) inoculation. The source and application dose of nitrogen fertilizer had varied impact on measured parameter. The maximum phosphorous and iron concentration were measured by soil inoculation with S4 and applying 200 ppm nitrate potassium nitrogen fertilizer. Application of 200 ppm KNO3 nitrogen fertilizer with different Streptomyces strains showed the capability of S2 in decreasing nitrate content while protein content increased. In particular, the strains S2 and S4 have great potential in being formulated and used as biofertilizers.
ARTICLE | doi:10.20944/preprints202204.0283.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: molecular ecology; functional diversity; DNA sequencing
Online: 28 April 2022 (10:31:56 CEST)
Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities’ response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and CO1 amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using DNA Subway, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r>0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi:bacteria (F:B) proportions between different trails (p=2*10^-16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema, and Tremella. Chlorellales algae, and pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella, were associated with the cluster. There was functional redundancy in clusters that were differently composed, but shared similar ecological functions. These results implied a set of traits for post fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, pathogenicity and parasitism, antimicrobials, and N-metabolism.
ARTICLE | doi:10.20944/preprints202303.0337.v1
Subject: Arts And Humanities, Classics Keywords: metabarcoding; statistical modeling; urban river ecology
Online: 20 March 2023 (03:30:47 CET)
In this study we sought to investigate the impact of urbanization, presence of concrete river bottom, and nutrient pollution on microbial communities along the L.A. River. Six molecular markers were evaluated for identification of bacteria, plants, fungi, fish, and invertebrates in 90 samples. PCA (principal components analysis) was used with PAM (partitioning around medoids) clustering to reveal community structure and an NB (Negative binomial) model in DESeq2 was used for differential abundance analysis. PCA and factor analysis exposed the main axes of variation but were sensitive to outliers. Differential abundance of Proteobacteria was associated with soft bottom sites, and there was an apparent balance in the abundance of organisms responsible for nitrogen cycling. Nitrogen cycling was explained by differential abundance of ammonia oxidizing archaea, the complete ammonia oxidizers Nitrospira sp., nitrate reducing bacteria Marmoricola sp., and nitrogen fixing bacteria Devosia sp. which were differentially abundant at soft-bottom sites (p adj < 0.002). In contrast, differential abundance of several Cyanobacteria and other anoxygenic phototrophs was associated with the concrete bottom sites, which suggested the accumulation of excess nitrogen. The soft bottom sites tended to be represented by differential abundance of aerobes, whereas the concrete-associated species tended to be alkaliphilic, saliniphilic, calciphilic, sulfate dependent, and anaerobic. In Glendale Narrows, downstream from multiple water reclamation plants, there were differential abundance of cyanobacteria and algae, however indicator species for low nutrient environments and ammonia-abundance were also present. There was differential abundance of ascomycetes associated with Arroyo Seco and a differential abundance of Scenedesmaceae green algae and cyanobacteria in Maywood, in the analysis which compared suburban with urban river communities. The proportion of Ascomycota to Basidiomycota within the LA River differed from the expected proportion based on published worldwide freshwater and river 18S data; the shift in community structure was most likely associated with the extremes of urbanization. This study indicates that extreme urbanization can result in overrepresentation of cyanobacterial species that could cause reductions in water quality and safety.