Molecular characterization of eukaryotic algal communities in the tropical phyllosphere based on real-time sequencing of the 18S rDNA gene

Seasonal variation in soil algal community structure in different forest plantations in subtropic China

Algae exert great impact on soil formation and biogeochemical cycling. However, there is no full understanding of the response of soil algal community structure to the seasonal fluctuations in temperature and moisture and changes of soil physicochemical properties across different forests. Here, based on 23S rRNA gene sequencing, we analyzed soil algal community structure in four different forest plantations in two seasons and examined soil physiochemical properties. The results showed the significantly seasonal variation in soil algal community structure, with the higher overall diversity in summer than in winter. In addition, there existed significant correlations between soil algae (species composition, relative abundance, diversity index) and physicochemical properties (pH, total phosphorus, organic matter and nitrate nitrogen), suggesting that edaphic characteristics are also largely responsible for the variation in soil algal community. Nevertheless, the seasonal variation in algal community structure was greater than the variation across different forest plantations. This suggest temperature and moisture are more important than soil physicochemical properties in determining soil algal community structure. The findings of the present study enhance our understanding of the algal communities in forest ecosystems and are of great significance for the management and protection of algal ecosystem.

Seven newly sequenced chloroplast genomes from the order Watanabeales (Trebouxiophyceae, Chlorophyta): Phylogenetic and comparative analysis

The little-known order Watanabeales currently includes 10 genera with Chlorella-like species that reproduce by unequal-sized autospores and are predominantly solitary or terrestrial. The taxonomic scheme of Watanabeales has only been primarily inferred by short and less informative rDNA phylogenetic analysis. In the present study, seven newly sequenced genomes and one reported chloroplast genome representing the existing major branches of Watanabeales were harvested to phylogenetically reconstruct this order and to further understand its evolution. All chloroplast genomes of Watanabeales ranging from 133 to 274 kb were circular mapping and lacked a quadripartite structure. The chloroplast genome size, GC content, number of introns, and length of intergenic region proportion of the Watanabeales showed consistent trends, with Calidiella yingdensis D201 and Kalinella pachyderma 2601 having the lowest and highest values, respectively, echoing the positive correlation between organismal size and genome size. Phylogenetic analysis of Watanabeales based on 76 protein-coding genes coupled with the establishment of various complex analytical methods determined the unique robust taxonomic scheme which was incongruent with rDNA. Comparative genomic analyses revealed that the chloroplast genomes of Watanabeales accounted for numerous complex rearrangements and inversions which indicated high cryptic diversity. Substitution rate estimation indicated that the chloroplast genomes of Watanabeales were under purifying selection and similar evolutionary pressure and supported the view that genus Symbiochloris should be excluded from Watanabeales. Our results enrich the chloroplast genome resources of Watanabeales, clarify the phylogenetic status of species within this order, and provide more reference information for subsequent taxonomic and phylogenetic study.

Phyllosphere eukaryotic microalgal communities in rainforests: Drivers and diversity

Phyllosphere algae are common in tropical rainforests, forming visible biofilms or spots on plant leaf surfaces. However, knowledge of phyllosphere algal diversity and the environmental factors that drive that diversity is limited. The aim of this study is to identify the environmental factors that drive phyllosphere algal community composition and diversity in rainforests. For this purpose, we used single molecule real-time sequencing of full-length 18S rDNA to characterize the composition of phyllosphere microalgal communities growing on four host tree species (Ficus tikoua, Caryota mitis, Arenga pinnata, and Musa acuminata) common to three types of forest over four months at the Xishuangbanna Tropical Botanical Garden, Yunnan Province, China. Environmental 18S rDNA sequences revealed that the green algae orders Watanabeales and Trentepohliales were dominant in almost all algal communities and that phyllosphere algal species richness and biomass were lower in planted forest than in primeval and reserve rainforest. In addition, algal community composition differed significantly between planted forest and primeval rainforest. We also found that algal communities were affected by soluble reactive phosphorous, total nitrogen, and ammonium contents. Our findings indicate that algal community structure is significantly related to forest type and host tree species. Furthermore, this study is the first to identify environmental factors that affect phyllosphere algal communities, significantly contributing to future taxonomic research, especially for the green algae orders Watanabeales and Trentepohliales. This research also serves as an important reference for molecular diversity analysis of algae in other specific habitats, such as epiphytic algae and soil algae.

New insights into engineered plant-microbe interactions for pesticide removal

Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.

The Diversity of Lichenized Trentepohlioid Algal (Ulvophyceae) Communities is Driven by Fungal Taxonomy and Ecological Factors

Trentepohliales are a group of both free-living and lichenized algae, with most diversity occurring in tropical regions. Recent studies showed that the abundance of lichens with a trentepohlioid photobiont has been increasing in temperate habitats, probably because of global warming, which makes them an interesting study case. A detailed molecular study of the diversity of lichenized Trentepohliales, epiphytic as well as epilithic, was performed in three forests of north-western Europe. Additional samples of lichens of the Arthoniales order (associating essentially with a trentepohlioid photobiont) from other European regions and from other continents were also sequenced. A total of 195 algal sequences were obtained. Phylogenetic analyses with rbcL and ITS loci were performed and associations between phylogenetic distances of photobionts and ecological factors (substratum, climate or Wirth indices, mycobiont taxonomy, and geographic location) were tested by variation partitioning and phylogenetic signal analyses. The high number of rbcL algal haplotypes found in some lichens or on different substrata revealed that the Trentepohliales diversity in extratropical regions was underestimated. The phylogenetic patterns showed selectivity of some photobionts in their fungal partner choice and vice-versa, while others were linked with several haplotypes. Photobionts seemed to be less selective than mycobionts. The main factors influencing lichenized algal community were climate and mycobiont species. Coevolution between mycobionts and photobionts as well as switching between free living and lichenized lifestyles appeared to drive the evolution of Trentepohliales and might explain the high cryptic diversity observed, which might be changing in some regions due to climate change.

Bacterial Communities in the Endophyte and Rhizosphere of White Radish (Raphanus sativus) in Different Compartments and Growth Conditions

Endophyte resources have important research value in multiresistance breeding, ecological protection, germicide development, and other fields. In this study, high-throughput sequencing (Illumina-MiSeq) technology was employed to analyse the diversity and community composition of white radish (Raphanus sativus) endophytes and rhizosphere bacteria in different compartments and cultivation conditions, including greenhouse and open field cultivation, at both the phylum and genus levels. Alpha diversity index analysis showed that the bacterial richness and diversity values of rhizosphere bacteria were higher than those of endophytes in different compartments. NMDS analysis and microbial co-occurrence network analysis showed that apart from the similarity in the endophytic bacterial composition of the leaf and root endosphere, the endophytic bacterial composition in flesh and epidermis of radish were also more similar. The dominant endophytic bacteria in white radish were Proteobacteria, Bacteroidetes, and Actinomycetes at the phylum level. We analyzed the effects of different ecological compartments and two cultivation environments on radish microorganisms, and found that ecological compartments played an important role, which was related to the mechanism of microbial assembly in plants. The same facility cultivation can also improve the diversity of radish microorganisms in different ecological compartments, and change the biomarkers that play a major role in rhizosphere microorganisms and endophytes of radish. Bacteria plays an important role in the process of plant growth, and the study of endophytes enriches the understanding of microbial diversity in white radish, which helps to provide insight into the ecological function and interaction mechanisms of plants and microorganisms.

New Species of Chloroidium (Trebouxiophyceae, Chlorophyta) from East Asia

Chlorella-like green algae that reproduce only asexually by immotile autospores or motile zoospores are the most typical inhabitants of non-aquatic environments. They have a simple morphology that hampers their differentiation, but algae of such habit represent a diverse array of lineages, which are mostly in the classes Chlorophyceae and Trebouxiophyceae. One of these lineages is the order Watanabeales (Watanabea clade; Trebouxiophyceae), which comprises 10 genera that share a distinct mode of reproduction through unequally sized autospores. Most of these genera account for a few species that are rarely recorded in nature. In contrast, the genus Chloroidium is one of the most species-rich and widely distributed members of the order. Three strains of coccoid green alga were isolated during a study of soil algae in the temperate monsoon climate zone of Asia. These strains are described here as a new species, Chloroidium orientalis. SSU and ITS rDNA sequence data, morphological characteristics, and life cycle features differentiate these strains from known members of the genus.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

Watanabeales ord. nov. and twelve novel species of Trebouxiophyceae (Chlorophyta)

The Trebouxiophyceae include Chlorellales, Prasiolales, Trebouxiales, Microthamniales, and numerous members for which taxonomic locations have not been determined. The Watanabea clade is a group in the Trebouxiophyceae of Chlorella-like taxa, which are predominantly solitary and terrestrial. With the increase in descriptions of new species within the Watanabea clade in recent years, it is necessary to define the boundary and taxonomic status of the clade. In this study, nineteen strains of terrestrial algae collected from China were investigated based on molecular and morphological data, involving phylogenetic analyses, light and electron microscopy, and ITS-2 secondary structures. These 19 strains were described as five known species and 12 novel ones. Based on the consistent topological structures of the phylogenetic analyses for three taxonomic levels (the core Chorophyta, Trebouxiophyceae based on 18S sequences, Watanabeales and Symbiochloris based on 18S, 5.8S, ITS2 and rbcL gene sequences) and common morphological characteristics, especially the key phenotypic feature of unequally sized autospores, the Watanabea clade was defined as a new order, Watanabeales ord. nov., with one family, Watanabeaceae fam. nov. The boundary of Watanabeales was delineated and included the genera Chloroidium, Calidiella, Jaagichlorella, Kalinella, Massjukichlorella, Mysteriochloris, Polulichloris, Phyllosiphon, Watanabea, and Viridiella. Symbiochloris did not belong to Watanabeales according to the phylogenetic analyses and the reproduction by equal-sized autospores, aplanospores, or zoospores. The Watanabeales were separated into four groups during the phylogenetic analyses, but no regular differences in habitats or morphology could be used as the morphological basis to split Watanabeales into the four groups.

Nutritional conditions of the novel freshwater Coccomyxa AP01 for versatile fatty acids composition

AIMS

This study was to analyse the biomass production and fatty acids (FAs) profiles in a newly isolated chlorophyte, namely Coccomyxa AP01, under nutritionally balanced (NB) conditions (comparing nitrate and urea as nitrogen sources) and nitrogen or phosphate deprivation.

METHODS AND RESULTS

Lipid yields was about 30%-40% of dried biomasses in all examined nutritional conditions. Under NB conditions, lipids were principally constituted by monounsaturated FAs, mainly represented by oleic acid, and saturated and polyunsaturated FAs at similar concentrations. Nutrients deprivation induced remarkable changes in FAs profiles, with the highest amounts of saturated (42%-46%), followed by similar amounts of monounsaturated and polyunsaturated, and the emergence of rare long-chain FAs. Under phosphate deprivation, biomass yield was similar to NB conditions, with the highest yield of saturated (mainly palmitic acid) and of polyunsaturated FAs (33%) (mainly linoleic and linolenic acids).

CONCLUSIONS

Balanced or deprived nutritional conditions in Coccomyxa AP01 induced a selective production and composition of FAs. The phosphate-deprivation condition concomitantly provided high biomass yield and the production of high value saturated and polyunsaturated FAs with industrial interest.

SIGNIFICANCE AND IMPACT OF THE STUDY

Coccomyxa AP01 could be considered a promising source of different FAs, including also docosapentaenoic acid, for several commercial purposes spanning from biodiesel production, pharmaceutical and cosmetic applications to innovative aquaculture fish feeds.

Algae as New Kids in the Beneficial Plant Microbiome

Previously, algae were recognized as small prokaryotic and eukaryotic organisms found only in aquatic habitats. However, according to a recent paradigm shift, algae are considered ubiquitous organisms, occurring in plant tissues as well as in soil. Accumulating evidence suggests that algae represent a member of the plant microbiome. New results indicate that plants respond to algae and activate related downstream signaling pathways. Application of algae has beneficial effects on plant health, such as plant growth promotion and disease control. Although accumulating evidence suggests that secreted compounds and cell wall components of algae induce physiological and structural changes in plants that protect against biotic and abiotic stresses, knowledge of the underlying mechanisms and algal determinants is limited. In this review, we discuss recent studies on this topic, and highlight the bioprotectant and biostimulant roles of algae as a new member of the plant beneficial microbiome for crop improvement.

Removal mechanisms of phosphorus in non-aerated microalgal-bacterial granular sludge process

Microalgal-bacterial granular sludge processes are attracting increasing research interest in fields of biological municipal wastewater treatment. However, these processes currently suffer from inefficient phosphorus removal and long hydraulic reaction time. As such, a self-sustaining synergetic microalgal-bacterial granular sludge process was explored for improving phosphorus removal. Results showed that about 86% of influent phosphorus could be removed within 6 h comprising 2-hr dark phase and 4-hr light phase. Slight phosphorus release was observed in dark phase, followed by a significant phosphorus uptake in light phase together with the accumulation of poly-phosphorus in microalgal cells. The analyses by PacBio's sequencing and fluorescence in situ hybridization revealed that microalgal genus of Pantanalinema were the major phosphorus-accumulating organisms. Based on these experimental observations, the removal mechanisms of phosphorus by microalgal-bacterial granular sludge process were identified. It is expected that this study may shed lights on the pathways of biological phosphorus removal in microalgal-bacterial granular sludge process.

A self-sustaining synergetic microalgal-bacterial granular sludge process towards energy-efficient and environmentally sustainable municipal wastewater treatment

Globally increasing concerns have been raised on the high energy consumption and greenhouse gas emissions in conventional municipal wastewater treatment processes over the past decades. In this study, a self-sustaining synergetic microalgal-bacterial granular sludge process was thus developed to address these challenges. The results showed that the microalgal-bacterial granular sludge process was capable of removing 92.69%, 96.84% and 87.16% of influent organics, ammonia and phosphorus under non-aeration conditions over a short time of 6 h. The effluent could meet the increasingly stringent discharge standards in many countries worldwide. A tight synergetic interrelationship effect between microalgae and bacteria in granules was essential for such excellent process performance. The stoichiometric and functional genes analyses further revealed that most of organic matter and nutrients were removed through microalgal and bacterial assimilations. Moreover, it was found that there existed a desirable distribution of functional species of microalgae and bacteria in microalgal-bacterial granules, which appeared to be essential for the self-sustaining synergetic reactions and stability of microalgal-bacterial granules. Consequently, this work may offer a promising engineering alternative with great potential to achieve energy-efficient and environmentally sustainable municipal wastewater treatment.

d-Lactic acid secreted by Chlorella fusca primes pattern-triggered immunity against Pseudomonas syringae in Arabidopsis

Biological control agents including microbes and their products have been studied as sustainable crop protection strategies. Although aquatic microalgae have been recently introduced as a biological control agent, the underlying molecular mechanisms are largely unknown. The aim of the present study was to investigate the molecular mechanisms underlying biological control by microalga Chlorella fusca. Foliar application of C. fusca elicits induced resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato DC3000 that activates plant immunity rather than direct antagonism. To understand the basis of C. fusca-triggered induced resistance at the transcriptional level, we conducted RNA sequencing (RNA-seq) analysis. RNA-seq data showed that, upon pathogen inoculation, C. fusca treatment primed the expression of cysteine-rich receptor-like kinases, WRKY transcription factor genes, and salicylic acid and jasmonic acid signalling-related genes. Intriguingly, the application of C. fusca primed pathogen-associated molecular pattern -triggered immunity, characterized by reactive oxygen species burst and callose deposition, upon flagellin 22 treatment. The attempts to find C. fusca determinants allowed us to identify d-lactic acid secreted in the supernatant of C. fusca as a defence priming agent. This is the first report of the mechanism of innate immune activation by aquatic microalga Chlorella in higher plants.

Bioinformatics analysis of endophytic bacteria related to berberine in the Chinese medicinal plant Coptis teeta Wall

Endophytic microorganisms absorb nutrients and prevent pathogen damage, supporting healthy plant growth. However, the relationship between endophytic bacteria and berberine synthesis in the medicinal plant Coptis teeta Wall. remains unclear. Herein, we explored the community composition of endophytic bacteria related to berberine in roots, stems, and leaves of wild-type and cultivated C. teeta. Endophytic bacterial communities were analyzed by 16S rRNA sequencing, and berberine content in roots was analyzed by high-performance liquid chromatography. Proteobacteria, Actinobacteria, and Bacteroidetes were the major phyla, and Mycobacterium, Salmonella, Nocardioides, Burkholderia-Paraburkholderia, and Rhizobium were the dominant genera in root, stem, and leaf tissues. Root berberine content was positively correlated with total N, total P, total K, and available K in rhizosphere soil. In addition, root berberine content was positively correlated with Microbacterium and norank_f_7B-8, whereas soil total K was positively correlated with Microbacterium and Burkholderia-Paraburkholderia in roots. Our results demonstrated a clear correlation between dominant endophytic bacteria and berberine synthesis in C. teeta. The findings are useful for the promotion of berberine production in C. teeta via manipulation of endophytic bacteria.

A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome

The plant leaf surface, or phyllosphere, represents a unique and challenging microbial biome with a diverse and dynamic community of commensal, parasitic, and mutualistic agents of microscopic proportions. This mini-review offers a digest of recently published research dedicated to the study of phyllosphere microbiota, framed in the context of processes and outcomes of microbial community assembly, structure, and (inter)activity in the phyllosphere, with particular focus on the contributions of environment, plant, and microbe, and on the potential benefits of interrogating those contributions at finer resolutions.

Fatty Acid Content and Profile of the Novel Strain of Coccomyxa elongata (Trebouxiophyceae, Chlorophyta) Cultivated at Reduced Nitrogen and Phosphorus Concentrations

A novel freshwater strain of Coccomyxa elongata (MZ-Ch64) was isolated from the Zaporizhia region, Ukraine. The identification was based on the phylogenetic analysis of SSU rDNA gene and ITS1-5.8S rDNA-ITS2 region and predicted secondary structure of the ITS2. Phylogenetic analysis placed this strain in the Coccomyxa group, within the class Trebouxiophyceae. The novel strain MZ-Ch64 formed a strongly supported lineage closest with C. elongata. The MZ-Ch64 strain differed from the morphological description of the species by the size of vegetative cells and absence of small mucilaginous caps at one end of the cell. A number of experiments with different concentrations of phosphate and nitrate were conducted to evaluate changes in the resulting fatty acid profiles and biomass productivity. The fatty acid profile and total fatty acids varied significantly under different nutrient deficiencies. The dominant fatty acid during cultivation on standard BBM medium, as well as in phosphorus-depleted conditions, was oleic acid (to 48.0%-54.6% of total fatty acids). Absence of nitrogen alone, and absence of both nitrogen and phosphorus, led to an increase of palmitic acid (to 24.7%-25.6%), cis-7-hexadecenoic acid (to 14.8%) and α-linolenic acid (to 9.1%-10.1%) in comparison with the control sample. The greatest variation was found for oleic acid (31.9%-54.6%). Thus, this strain can be considered as a potential producer of oleic acid or cis-7-hexadecenoic and α-linolenic acids for biotechnological applications.

The importance of cyanobacteria and microalgae present in aerosols to human health and the environment - Review study

Airborne microalgae and cyanobacteria are among the least studied organisms in aerobiology. While those of them living in freshwater and seawater are well recognized, those constituting the components of aerosols are rarely the focus of research. However, their presence has been noted by scientists from all over the world. The presence of these organisms is not indifferent to the environment as they participate in the formation of clouds and influence both the hydrological cycle and Earth's climate. Recent studies have concentrated mostly on the negative impact of airborne cyanobacteria and microalgae, as well as the toxic compounds they produce, on human health. This review focuses on measurement results published on those bioaerosols, combining the achievements of scientists from the last century with the latest reports and trends. Within it gaps in current knowledge are discussed, including the role of airborne organisms in the transport of harmful chemicals like PAHs and heavy metals. The current studies on which it is based emphasize the advantages and disadvantages of the measurement methods used in sampling and analysing. It also visualizes, in the form of maps, where research on bioaerosols has so far been conducted, while at the same time determining the share of organisms potentially dangerous to human health. In addition, we have also tried to recommend future research directions for both environmental and laboratory-based studies.