Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem

Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning

Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.

Microbiomes of air dust collected during the ground-based closed bioregenerative life support experiment "Lunar Palace 365"

BACKGROUND

Understanding the dynamics of airborne microbial communities and antibiotic resistance genes (ARGs) in space life support systems is important because potential pathogens and antibiotic resistance pose a health risk to crew that can lead to mission failure. There have been few reports on the distribution patterns of microbiomes and ARGs in space life support systems. In particular, there have been no detailed investigations of microbiomes and/or antibiotic resistance based on molecular methods in long-term confined bioregenerative life support systems (BLSSs). Therefore, in the present study, we collected air dust samples from two crew shifts, different areas, and different time points in the "Lunar Palace 365" experiment. We evaluated microbial diversity, species composition, functional potential, and antibiotic resistance by combining cultivation-independent analyses (amplicon, shot-gun sequencing, and qPCR).

RESULTS

We found that the bacterial community diversity in the Lunar Palace1 (LP1) system was higher than that in a controlled environment but lower than that in an open environment. Personnel exchange led to significant differences in bacterial community diversity, and source tracking analysis revealed that most bacteria in the air derived from the cabin crew and plants, but no differences in microbial function or antibiotic resistance were observed. Thus, human presence had the strongest effect on the succession of microbial diversity in the BLSSs.

CONCLUSIONS

Our results highlight that microbial diversity in BLSSs is heavily influenced by changes in crew and is unique from other open and controlled environments. Our findings can be used to help develop safe, enclosed BLSS that meet the requirements of human survival and habitation in outer space. In addition, our results can further enhance our understanding of the indoor air microbial community and effectively maintain a safe working and living environment, including plant growth.

Dynamic changes in rhizosphere fungi in different developmental stages of wheat in a confined and isolated environment

As the core food crop of a bioregenerative life support system (BLSS), wheat is susceptible to pathogen infection due to the lack of effective microbial communities in the confined and isolated environment. Therefore, a thorough understanding of the dynamic changes in wheat rhizosphere fungi is of great significance for improving wheat production and ensuring the stability of the BLSS. In the current study, we collected samples of rhizosphere fungi in the four growth stages of wheat grown in the "Lunar Palace 365" experiment. We employed bioinformatics methods to analyze the samples' species composition characteristics, community network characteristics, and FUNGuild function analysis. We found that the species composition of rhizosphere fungi in the wheat at the tillering stage changed greatly in the closed and isolated environment, while the species composition in the seedling, flowering, and mature stage were relatively stable. The results of the FUNGuild function analysis showed that the functions of rhizosphere fungi changed during wheat development. The rhizosphere fungal community was centered on Ascomycota, Mortierellomycota, and Chytridiomycota, and the community showed the characteristics of a "small world" arrangement. The stage of wheat seedlings is characterized by a greater abundance, diversity, and complexity of the network of interactions in the rhizosphere mycorrhiza community, while the tillering stage exhibited a greater clustering coefficient. Based on the changes in species composition, guild function regulation, and community structure differences of the wheat rhizosphere fungi in the BLSS, our study identified the critical fungal species during wheat development, providing a reference for ensuring the health and yield of plants in the BLSS system. KEY POINTS: • The diversity, composition, FUNguild, and network structure of rhizosphere fungi were analyzed. • Ascomycota, Mortierellomycota, and Chytridiomycota were the center of the rhizosphere fungal community network. • The effects of different wheat developmental stages on the community composition, function, and network structure of rhizosphere fungi were examined.

Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments

Wheat is the core food crop in bioregenerative life support systems (BLSSs). In confined isolation environments, wheat growth suffers from a lack of stable microbial communities and is susceptible to pathogenic infections due to the culture substrate's limitations. To overcome this limitation, the time series changes of wheat rhizosphere microorganisms in wheat production must be understood. In the present study, we examined the rhizosphere microbial samples from wheat at four different growth stages from plants collected from a BLSS plant cabin. We employed bioinformatics analysis strategies to analyze the characteristics of species composition, function prediction, and community network. The species composition of wheat rhizosphere microorganisms was relatively stable in the seedling, tillering, and flowering stages in confined isolation environments. However, we observed marked microbial changes at mature stages. The results of functional prediction analysis suggest that the rhizosphere microbial community function of "Energy metabolism" gradually decreased, and the function of "Transmembrane transport" gradually increased during wheat development. The construction of the rhizosphere microbial community is non-random, scale-free and has the characteristics of a small world. We found the tillering stage to be more complex than the other stages. Our study reveals the composition characteristics, functional changes, and community structure fluctuations of rhizosphere bacteria at different development stages of wheat in the isolated and controlled environment, providing a theoretical basis for the efficient production of BLSS plant systems. KEY POINTS: • We collected wheat rhizosphere microorganisms at different stages in a confined isolation environment. • The diversity, composition, function, and network structure of rhizosphere bacteria were analyzed. • The effect of different wheat stages on the composition, function, and network structure of rhizosphere microorganisms was speculated.

Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence

Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant snow mold resistance are not elucidated. Our study aimed to identify comprehensive characteristics of a local community of snow mold-causing Microdochium species colonizing a particular crop culture. By using the next-generation sequencing (NGS) technique, we characterized fungal and bacterial communities of pink snow mold-affected winter rye (Secale cereale) plants within a given geographical location shortly after snowmelt. Twenty-one strains of M. nivale were isolated, classified on the basis of internal transcribed spacer 2 (ITS2) region, and characterized by morphology, synthesis of extracellular enzymes, and virulence. Several types of extracellular enzymatic activities, the level of which had no correlations with the degree of virulence, were revealed for Microdochium species for the first time. Our study shows that genetically and phenotypically diverse M. nivale strains simultaneously colonize winter rye plants within a common area, and each strain is likely to utilize its own, unique strategy to cause the disease using "a personal" pattern of extracellular enzymes.

The effect of wheat seedling density on photosynthesis may be associated with the phyllosphere microorganisms

Wheat seedlings are significantly impacted by the presence of bacteria. However, bacteria are unavoidably growing together with wheat. The study aimed to reveal wheat photosynthesis, phyllosphere bacterial community composition, and a shift in the bacterial community following different density treatments in a closed artificial ecosystem. Here, we report the relationship between photosynthesis and bacterial community in wheat seedlings for different planting densities. In this closed artificial ecosystem, a total of 30 phyla were detected, with 17 of them were simultaneously present in four treatments, under high light intensity and carbon dioxide growth environment. The key phyla detected include Firmicutes, Proteobacteria, and Bacteroidetes. We found that planting densities significantly impacted the photosynthetic characteristics of wheat and bacterial genetic biodiversity, but not on species composition of the bacterial community. Network analysis shows that the phyllosphere bacteria network structures were characterized by the clustering coefficient and modularity. Network for the 1000 plants/m² treatment group exhibits the highest levels of average clustering coefficient but lowest modularity and number of modules, among all plant densities tested. In addition, the network for the 1200 plants/m² treatment group exhibits the best characteristics in terms of net photosynthesis rate and intrinsic water use efficiency, higher complex phyllosphere community network structures, higher abundance of Corynebacterium, and more function of "Amino acid metabolism", which encourages the plants to grow better. The findings presented in this work elucidated the role of plant density in the growth of phyllosphere bacteria during wheat seedlings and provided theoretical support for reasonable wheat density cultivation in closed artificial ecosystems and wheat field production.

Effect of solid waste fermentation substrate on wheat (Triticum aestivum L.) growth in closed artificial ecosystem

Bioregenerative Life Support System (BLSS) is a closed artificial ecosystem and could provide oxygen, food, water and other substrates for long-term deep space survival. The treatment and recycle of the solid waste are crucial and rate-limiting steps in BLSS, and it's reported that the solid waste such as the inedible plants and human feces could be fermented aerobically and then reused as fertilizer for growing plants in BLSS, which may be an effective way to improve the solid waste recycling rate. However, the recycling performance and the effect on the system need to be evaluated. In this study, the fermented and decomposed solid waste product from the 365d BLSS experiment with human involved in Lunar Palace 1 was utilized, and was added to the Hoagland nutrient solution as a supplementary fertilizer in the weight proportion of 5% and 10%, respectively, for the cultivation of wheat (Group-5% and Group-10%). Then, the effects on wheat germination, morphology, photosynthesis, biomass, the conductivity of the cultured substrates and microorganisms were detected and compared with those of the CK group cultured using only Hoagland nutrient solution. The results showed that this planting method had no inhibitory effect on the wheat germination, root length and yield, and might even promote the vegetative growth of wheat in terms of Vigor index, plant height, leaf area and net photosynthesis rate to some extent. The added solid waste fermentation substrate as well as the planting environment in Lunar Palace 1 both had significant influences on the rhizosphere microorganisms of wheat. The bacteria diversity was more abundant than fungi at phylum level, and the relative abundance varied along with the wheat growth period. The relative abundance of the cellulose degrading microorganisms including Actinobacteria and Ascomycota increased in Group-5% and Group-10% compared with CK group along with the growth of wheat. Moreover, the proper reuse of the fermentation substrate could reduce the use of inorganic salts by 9.8%-11.9% and save 40L•m ^- 2 of water for wheat cultivation. This research has considerable application significance in future deep space exploration.

Semi-continuous fermentation of solid waste in closed artificial ecosystem: Microbial diversity, function genes evaluation

Bioregenerative Life Support System (BLSS) is a closed artificial ecosystem and could provide oxygen, food, water and other substances for space survival. Solid waste treatment is a key rate-limiting step in BLSS. In this study, solid wastes including wheat straw, human and yellow mealworm feces were disposed in a semi-continuous bio-convertor for 105 days in a ground-based experimental BLSS platform (Lunar Palace 1). Solid wastes at different periods were sampled and the microbial community variation, functional genes and metabolic pathways were analyzed. The results showed phyla Firmicutes, Bacteroidetes and Proteobacteria predominated in all samples. While microbial community structures at genus level were significantly different, indicating selective enrichment during the 105-day process. The abundance of functional gene related to carbohydrate transport and metabolism was predicted higher on 45-day and 70-day. The metabolic pathway analysis revealed the degradation mechanisms and provided evidence for metabolic regulation.

Plant microbiome analysis after Metarhizium amendment reveals increases in abundance of plant growth-promoting organisms and maintenance of disease-suppressive soil

The microbial community in the plant rhizosphere is vital to plant productivity and disease resistance. Alterations in the composition and diversity of species within this community could be detrimental if microbes suppressing the activity of pathogens are removed. Species of the insect-pathogenic fungus, Metarhizium, commonly employed as biological control agents against crop pests, have recently been identified as plant root colonizers and provide a variety of benefits (e.g. growth promotion, drought resistance, nitrogen acquisition). However, the impact of Metarhizium amendment on the rhizosphere microbiome has yet to be elucidated. Using Illumina sequencing, we examined the community profiles (bacteria and fungi) of common bean (Phaseolus vulgaris) rhizosphere (loose soil and plant root) after amendment with M. robertsii conidia, in the presence and absence of an insect host. Although alpha diversity was not significantly affected overall, there were numerous examples of plant growth-promoting organisms that significantly increased with Metarhizium amendment (Bradyrhizobium, Flavobacterium, Chaetomium, Trichoderma). Specifically, the abundance of Bradyrhizobium, a group of nitrogen-fixing bacteria, was confirmed to be increased using a qPCR assay with genus-specific primers. In addition, the ability of the microbiome to suppress the activity of a known bean root pathogen was assessed. The development of disease symptoms after application with Fusarium solani f. sp. phaseoli was visible in the hypocotyl and upper root of plants grown in sterilized soil but was suppressed during growth in microbiome soil and soil treated with M. robertsii. Successful amendment of agricultural soils with biocontrol agents such as Metarhizium necessitates a comprehensive understanding of the effects on the diversity of the rhizosphere microbiome. Such research is fundamentally important towards sustainable agricultural practices to improve overall plant health and productivity.

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi

High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.

Variations in Fungal Community and Diversity in Doushen With Different Flavors

Doushen, a traditional Chinese fermented soybean product, may be spiced or spicy depending on whether pepper powder is added. While numerous studies have investigated the microbial communities of other fermented foods, little is known on the fungal diversity of Doushen. Therefore, in this study, we investigated the fungal community and diversity in both spiced and spicy Doushen. Our results revealed that fungal species richness significantly differed between the samples with different flavors. A total of nine phyla and 188 fungal genera were identified, and Ascomycota and Aspergillus were predominant in all samples. Based on linear discriminant analysis, a total of 57 OTUs were significantly different between the two samples. Results of non-metric multidimensional scaling and unweighted pair-group analysis suggested that the presence of pepper powder affects the microbial community in Doushen. Network analysis showed that microbial interactions between fungal communities in Doushen with different flavors were significantly different. The results on the enumeration and identification of fungi were consistent with the composition of the dominant genera in the samples with different flavors. This study provides a theoretical basis for future research on food ecology in Doushen.

Community Structure, Diversity and Potential of Endophytic Bacteria in the Primitive New Zealand Medicinal Plant Pseudowintera colorata

Although the importance of the plant microbiome in commercial plant health has been well established, there are limited studies in native medicinal plants. Pseudowintera colorata (horopito) is a native New Zealand medicinal plant recognized for its antimicrobial properties. Denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq analysis of P. colorata plants from ten sites across New Zealand showed that tissue type strongly influenced the diversity and richness of endophytic bacteria (PERMANOVA, P < 0.05). In addition, two OTUs belonging to the genus Pseudomonas (Greengenes ID: 646549 and 138914) were found to be present in >75% of all P. colorata leaf, stem and root samples and were identified as the members of the P. colorata “core endomicrobiome”. Culture-independent analysis was complemented by the recovery of 405 endophytic bacteria from the tissues of P. colorata. Some of these cultured endophytic bacteria (n = 10) showed high antagonism against four different phytopathogenic fungi tested. The influence of endophytic bacteria on plant growth was assessed by inoculating P. colorata seedlings. The mean shoot height of seedlings treated with Bacillus sp. TP1LA1B were longer (1.83×), had higher shoot dry weight (1.8×) and produced more internodes (1.8×) compared to the control.

Characterization of rhizosphere bacterial community and berry quality of Hutai No.8 (Vitis vinifera L.) with different ages, and their relations

BACKGROUND

Rhizosphere soil microbial communities play an important role in grapevine growth. However, the relationship of the rhizosphere soil bacterial community and berry quality of Hutai No.8 grape with different tree-ages is unclear. In this work, the Biolog-ECO technique was used to explore the functional diversity of the rhizosphere soil bacterial communities of Hutai No.8 grape with five ages (3, 5, 7, 9 and 11 years old). Meanwhile, grape berry quality indicators related to berry appearance, flavor and functional substance quality was also examined.

RESULTS

Principal component analysis of grape berry quality mainly separated 3-year-old (first bear fruit) and the other tree-ages. In particular, peel weight and total soluble solid content of 3-year-old grape berry was significantly less than that of others. Furthermore, average well color development, species richness and Shannon's diversity index increased significantly with grapevine age. Moreover, the metabolic activities and functional diversity of soil microbial communities in using carbon sources were significantly increasing with grapevine age. Moreover, there were significant correlation between physicochemical indices of grape berry quality and six functional categories of carbon sources.

CONCLUSION

Tree-ages could greatly affect the rhizosphere microbial community structure and richness, and then affect the grape berry quality. © 2019 Society of Chemical Industry.

Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings

Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study, we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonisation by other microorganisms. We characterised an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial microorganisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.

The impact of the omics era on the knowledge and use of Lysobacter species to control phytopathogenic micro-organisms

Omics technologies have had a tremendous impact on underinvestigated genera of plant disease biocontrol agents such as Lysobacter. Strong evidence of the association between Lysobacter spp. and the rhizosphere has been obtained through culture-independent methods, which has also contributed towards highlighting the relationship between Lysobacter abundance and soil suppressiveness. It is conceivable that the role played by Lysobacter spp. in soil suppressiveness is related to their ability to produce an impressive array of lytic enzymes and antibiotics. Indeed, genomics has revealed that biocontrol Lysobacter strains share a vast number of genes involved in antagonism activities, and the molecular pathways underlying how Lysobacter spp. interact with the environment and other micro-organisms have been depicted through transcriptomic analysis. Furthermore, omics technologies shed light on the regulatory pathways governing cell motility and the biosynthesis of antibiotics. Overall, the results achieved so far through omics technologies confirm that the genus Lysobacter is a valuable source of novel biocontrol agents, paving the way for studies aimed at making their application in field conditions more reliable.

Plant probiotic bacteria enhance the quality of fruit and horticultural crops

The negative effects on the environment and human health caused by the current farming systems based on the overuse of chemical fertilizers have been reported in many studies. By contrast, bacterial inoculations produce positive effects on yields without causing this type of harm. Hence, during recent years, the commercialization of biofertilizers has been on the increase, and the number of companies and products available are expanding worldwide every year. In addition to the notable enhancement of crop production, many studies have shown how the application of bacteria has positive effects on food quality such as improved vitamin, flavonoid and antioxidant content, among other benefits. This advantage is interesting with respect to food that is consumed raw, such as fruits and many vegetables, as these bioactive molecules are maintained up until the moment the food is consumed. As regards this review focuses on the collection of studies that demonstrate that microorganisms can act as plant probiotics of fruit and horticultural crops, essential types of food that form part of a healthy diet.

The Bacterial Signature of Leptospermum scoparium (Mānuka) Reveals Core and Accessory Communities with Bioactive Properties

Leptospermum scoparium or mānuka is a New Zealand native medicinal plant that produces an essential oil with antimicrobial properties. This is the first study to investigate the structure and bioactivity of endophytic bacteria in mānuka by using a combination of cultivation-independent (DGGE) and dependent approaches. A total of 23 plants were sampled across three sites. Plants were considered either immature (3-8 years) or mature (>20 years). The endophyte community structure and richness was affected by plant tissue and bacterial communities became more stable and uniform as plant maturity increased. A total of 192 culturable bacteria were recovered from leaves, stems and roots. Some bacterial isolates showed in vitro biocontrol activity against two fungal pathogens, Ilyonectria liriodendri and Neofusicoccum luteum and a bacterial pathogen, Pseudomonas syringae pv. actinidiae. A high proportion of bacterial endophytes could produce siderophores and solubilise phosphate in vitro. Gammaproteobacteria was the most variable class, representing the majority of cultivated bacteria with bioactivity.