Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition?

The fate of plastic wraps in constructed wetland: Surface structure and microbial community

The high use of plastic wraps leads to significant environmental pollution. In this study, the surface structure and microbial community evolution of commercially available plastic wraps [polyethylene (PE), polyvinyl chloride (PVC), polyvinylidene chloride (PVDC), and polylactic acid (PLA)] in constructed wetlands (CWs) were investigated. The results indicated that all plastic wraps gradually decreased in molecular weight, crystallinity, melting, and crystallization temperatures, whereas a gradual increase was observed in the surface roughness, polymer dispersity index (PDI), carbonyl index (CI) and Shannon index of microorganisms colonizing the CWs. The aging rate of the plastic wrap was in the order: PLA > PVC > PE > PVDC, at the same site in the CWs, and it was in the order: soil surface > plant roots > subsoil, for the same plastic wrap. The diversity of microorganisms colonizing the same plastic wrap was in the order: plant roots > subsoil > soil surface. The Shannon indices of microorganisms on plastic wraps were lower than those in the soil, indicating that the diversity of microorganisms colonizing plastic wraps is limited. Additionally, the microbial community structure on the plastic surface was co-differentiated by the plastic type, placement position in the CWs, and aging time. Significantly different microbial community structures were found on the PVC and PVDC wrap surfaces, revealing that the chlorine in plastics limits microbial diversity. Unclassified members of Rhizobiaceae and Pseudomonadaceae were the dominant genera on the surface of the plastic wraps, suggesting that they may be the microorganisms involved in plastic degradation processes. The study provides valuable perspectives to facilitate a comprehensive understanding of the migration, fate, and environmental risks associated with microplastics (MPs) in wetlands.

Uncovering Interactions between Plant Metabolism and Plant-Associated Bacteria in Huanglongbing-Affected Citrus Cultivars Using Multiomics Analysis and Machine Learning

Huanglongbing (HLB) is a highly destructive disease that inflicts significant economic losses on the citrus industry worldwide but with no cure available. However, microbiomes formulated by citrus plants may serve as disease antagonists, increasing the level of HLB tolerance. This study established an integrated analysis of untargeted metabolomics and microbiomics data for different citrus cultivars, providing critical insights into the interactions between plant metabolism and plant-associated bacteria in the development of HLB. Machine learning models were applied to screen important metabolites and bacteria in multiple citrus materials, and the selected metabolites were then analyzed to identify essential pathways enriched in the plant and to correlate with the selected bacteria. Results demonstrated that the regulation of plant pathways, especially ABC transporters and ubiquinone and other terpene-ubiquinone biosynthesis pathways, could affect the microbial community structure, indicating potential solutions for controlling HLB by modulating bacteria in citrus plants or breeding tolerant citrus cultivars.

Ozone pollution, water deficit stress and time drive poplar phyllospheric bacterial community structure

Ground-level ozone (O₃) pollution often rise in the summer and coincide with drought stress, which alters the relationships between trees and associated microbial communities in a manner that can have pronounced effects on associated biological activity and ecosystem integrity. Discerning the responses of phyllosphere microbial communities to O₃ and water deficit could highlight the ability of plant-microbe interactions to either exacerbate or mitigate the effects of these stressors. Accordingly, this study was designed as the first report to specifically interrogate the impacts of elevated O₃ and water deficit stress on phyllospheric bacterial community composition and diversity in hybrid poplar saplings. Significant reductions in phyllospheric bacterial alpha diversity indices were observed, with clear evidence of significant time × water deficit stress interactions. The combination of elevated O₃ and water deficit stress shifted in the bacterial community composition over sampling time, resulted in significant increases in the relative abundance of the dominant Gammaproteobacteria phyla together with reductions in Betaproteobacteria. An increased prevalence of Gammaproteobacteria may represent a potential diagnostic dysbiosis-related biosignature associated with poplar disease risk. Significant positive correlations were observed between both Betaproteobacteria abundance and diversity indices and key foliar photosynthetic traits and isoprene emissions, whereas these parameters were negatively correlated with Gammaproteobacteria abundance. These findings suggest that the photosynthesis-related properties in plant leaves are closely related to the makeup of the phyllosphere bacterial community. These data provide novel insight into how plant-associated microbes can help maintain plant health and the stability of the local ecosystem in O₃-polluted and dried environments.

Response of the plant core microbiome to Fusarium oxysporum infection and identification of the pathobiome

Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can significantly advance our understanding of microbial-microbial interactions and consequences for disease progression and host functions. In this study, we combined glasshouse and field studies to analyse the soil and plant rhizosphere microbiome of cotton plants (Gossypium hirsutum) in the presence of a cotton-specific fungal pathogen, Fusarium oxysporum f. sp. vasinfectum (FOV). We found that FOV directly and consistently altered the rhizosphere microbiome, but the biocontrol agents enabled microbial assemblages to resist pathogenic stress. Using co-occurrence network analysis of the core microbiome, we identified the pathobiome comprised of the pathogen and key associate phylotypes in the cotton microbiome. Isolation and application of some negatively correlated pathobiome members provided protection against plant infection. Importantly, our field survey from multiple cotton fields validated the pattern and responses of core microbiomes under FOV infection. This study advances key understanding of core microbiome responses and existence of plant pathobiomes, which provides a novel framework to better manage plant diseases in agriculture and natural settings. This article is protected by copyright. All rights reserved.

Effects of elevated ozone on bacterial communities inhabiting the phyllo- and endo-spheres of rice plants

To explore the effects of elevated ozone (O₃) on microbial communities inhabiting phyllo- and endo-spheres of Japonica rice leaves, cultivars Nangeng 5055 (NG5055) and Wuyujing 27 (WYJ27) were grown in either charcoal-filtered air (CF) or elevated O₃ (ambient O₃ + 40 ppb, E-O₃) in field open-top chambers (OTCs) during a growing season. E-O₃ increased the values of the Shannon (43-80%) and Simpson (34-51%) indexes of the phyllo-and endo-spheric bacterial communities in NG5055. E-O₃ also increased the values of the phyllosphere Simpson index by 58% and the endosphere Shannon index by 54% in WYJ27. Both diversity indexes positively correlated with the contents of nitrogen, phosphorus, magnesium, and soluble sugar, and negatively correlated with the contents of starch and condensed tannins. The leaf-associated bacterial community composition significantly changed in both rice cultivars under E-O₃. Moreover, the leaf-associated bacterial communities in NG5055 were more sensitive to E-O₃ than those in WYJ27. The chemical properties explained 70% and 98% of variations in the phyllosphere and endosphere bacterial communities, respectively, suggesting a predominant role of chemical status for the endospheric bacterial community. Most variation (57.3%) in the endosphere bacterial community assembly was explained by phosphorus. Gammaproteobacteria and Pantoea were found to be the most abundant class (63-76%) and genus (38-48%) in the phyllosphere and endosphere, respectively. E-O₃ significantly increased the relative abundance of Bacteroidetes in the phyllosphere bacterial community and decreased the relative abundance of Gammaproteobacteria in the endophytic community. In conclusion, elevated O₃ increased the diversity of bacterial communities of leaf phyllosphere and endosphere, and leaf chemical properties had a more pronounced effect on the endosphere bacterial community.

Legumes of the Sardinia Island: Knowledge on Symbiotic and Endophytic Bacteria and Interactive Software Tool for Plant Species Determination

A meta-analysis was carried out on published literature covering the topic of interactive plant microbiology for botanical species of legumes occurring within the boundary of the Italian island Sardinia, lying between the Tyrrhenian and the western Mediterranean seas. Reports were screened for the description of three types of bacterial occurrences; namely, (a) the nitrogen-fixing symbionts dwelling in root nodules; (b) other bacteria co-hosted in nodules but having the ancillary nature of endophytes; (c) other endophytes isolated from different non-nodular portions of the legume plants. For 105 plant species or subspecies, over a total of 290 valid taxonomical descriptions of bacteria belonging to either one or more of these three categories were found, yielding 85 taxa of symbionts, 142 taxa of endophytes in nodules, and 33 in other plant parts. The most frequent cases were within the Medicago, Trifolium, Lotus, Phaseolus, and Vicia genera, the majority of symbionts belonged to the Rhizobium, Mesorhizobium, Bradyrhizobium, and Sinorhizobium taxa. Both nodular and extra-nodular endophytes were highly represented by Gammaproteobacteria (Pseudomonas, Enterobacter, Pantoea) and Firmicutes (Bacillus, Paenibacillus), along with a surprisingly high diversity of the Actinobacteria genus Micromonospora. The most plant-promiscuous bacteria were Sinorhizobium meliloti as symbiont and Bacillus megaterium as endophyte. In addition to the microbial analyses we introduce a practical user-friendly software tool for plant taxonomy determination working in a Microsoft Excel spreadsheet that we have purposely elaborated for the classification of legume species of Sardinia. Its principle is based on subtractive keys that progressively filter off the plants that do not comply with the observed features, eventually leaving only the name of the specimen under examination.

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

PREMISE

Within a broader study on leaf fossilization in freshwater environments, a long-term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis.

METHODS

We extracted surface-associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits.

RESULTS

Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition.

DISCUSSION

The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram-positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition.

Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics

Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3-V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02809-5.

Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens

The structure and function of rhizosphere microbial communities are affected by the plant health status. In this study, we investigated the effect of root rot on the avocado rhizosphere microbiome, using 16S rDNA and ITS sequencing. Furthermore, we isolated potential fungal pathogens associated with root rot symptoms and assessed their pathogenic activity on avocado. We found that root rot did not affect species richness, diversity or community structure, but induced changes in the relative abundance of several microbial taxa. Root rot increased the proportion of Pseudomonadales and Burkholderiales in the rhizosphere but reduced that of Actinobacteria, Bacillus spp. and Rhizobiales. An increase in putative opportunistic fungal pathogens was also detected in the roots of symptomatic trees; the potential pathogenicity of Mortierella sp., Fusarium spp., Lasiodiplodia sp. and Scytalidium sp., is reported for the first time for the State of Veracruz, Mexico. Root rot also potentially modified the predicted functions carried out by rhizobacteria, reducing the proportion of categories linked with the lipid and amino-acid metabolisms whilst promoting those associated with quorum sensing, virulence, and antibiotic resistance. Altogether, our results could help identifying microbial taxa associated to the disease causal agents and direct the selection of plant growth-promoting bacteria for the development of biocontrol microbial consortia.