https://web.science.uu.nl/pmi/publications/PDF/2012/TiPS-Berendsen-2012.pdf

The rhizosphere microbiome and plant health

The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.

Going back to the roots: the microbial ecology of the rhizosphere.

The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand, potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions, we can learn about the impact that fungi presently have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of this review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases, there are indications of fungal specific selection in fungus-associated bacteria, and possible mechanisms for such selection are discussed.

Living in a fungal world: impact of fungi on soil bacterial niche development⋆

Biological control involves the use of beneficial organisms, their genes, and/or products, such as metabolites, that reduce the negative effects of plant pathogens and promote positive responses by the plant. Disease suppression, as mediated by biocontrol agents, is the consequence of the interactions between the plant, pathogens, and the microbial community. Antagonists belonging to the genus Trichoderma are among the most commonly isolated soil fungi. Due to their ability to protect plants and contain pathogen populations under different soil conditions, these fungi have been widely studied and commercially marketed as biopesticides, biofertilizers and soil amendments. Trichoderma spp. also produce numerous biologically active compounds, including cell wall degrading enzymes, and secondary metabolites. Studies of the three-way relationship established with Trichoderma, the plant and the pathogen are aimed at unravelling the mechanisms involved in partner recognition and the cross-talk used to maintain the beneficial association between the fungal antagonist and the plant. Several strategies have been used to identify the molecular factors involved in this complex tripartite interaction including genomics, proteomics and, more recently, metabolomics, in order to enhance our understanding. This review presents recent advances and findings regarding the biocontrol-resulting events that take place during the Trichoderma –plant–pathogen interaction. We focus our attention on the biological aspects of this topic, highlighting the novel findings concerning the role of Trichoderma in disease suppression. A better understanding of these factors is expected to enhance not only the rapid identification of effective strains and their applications but also indicate the potentials for improvement of natural strains of Trichoderma .

Trichoderma–plant–pathogen interactions

Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions. In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.

Plant–microbiome interactions: from community assembly to plant health

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

Microbial Community Composition Affects Soil Fungistasis

The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.

Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

Anti-fungal properties of chitinolytic soil bacteria may enable them to compete successfully for chitin with fungi Additionally, the production of chitinase may be part of a lytic system that enables the bacteria to use living hyphae rather than chitin as the actual growth substrate, since chitin is an important constituent of most fungal cell walls Lysis of living fungal hyphae by chitinolytic bacteria has been reported frequently; however, these reports nearly always deal with bacteria that had been selected because of their mycolytic properties Our main objective was to get a better understanding of the relationship between chitinolytic and anti-fungal properties of bacteria that occur naturally in soils, ie without artificial selection Three inner dune sites, two of which were lime-poor and one lime-rich, along the Dutch coast were selected for this study Bacteria that were able to degrade colloidal chitin in water–agar comprised 02–57% of the total amount of culturable bacteria of these dune sites Pseudomonas spp were the most abundant culturable, chitin-degrading bacteria at the lime-poor sites, whereas Xanthomonas spp and Cytophaga spp were important at the lime-rich site Chitinolytic actinomycetes were relatively abundant at all three sites Chitinolytic and non-chitinolytic bacteria were randomly selected and tested for the possession of antagonistic activities against fungal dune strains [ Chaetomium globosum , Fusarium culmorum , F oxysporum , Idriella (Microdochium) bolleyi , Mucor hiemalis , Phoma exigua , Ulocladium sp] The tests were done using water–agar to simulate the energy-limiting conditions that bacteria will encounter in dune soils The percentage of bacterial isolates that were antagonistic against these fungi was considerably higher for chitinolytic strains than for non-chitinolytic ones Therefore, the possible involvement of chitinase with respect to the inhibition of fungal growth was studied in more detail It appeared that in many cases the inhibition of fungal growth was not accompanied by bacterial chitinase production There was also no clear relationship between the activity of other cell wall degrading enzymes ( β -1,3-glucanase and protease) and antagonism Chitinolytic bacteria had selective rather than general anti-fungal properties, which were not necessarily related to differences in general susceptibility of the fungi towards antagonism These results may indicate that antibiotics were involved in the antagonistic activities of chitinolytic bacteria against fungi Only growing fungi were antagonized by the chitinolytic bacteria; none of the chitinolytic bacteria were able to lyse existing mycelium of any of the fungi The relevance of the results for the ecology of chitinolytic soil bacteria is discussed

Anti-fungal properties of chitinolytic dune soil bacteria

A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C-16:0, C(16:1)omega7c and C(18:1)omega7c. DNA G + C contents were 57-62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (> 98.6% sequence similarity) and could be assigned to the beta-Proteobacteria, family 'Oxalobacteraceae', order 'Burkholderiales'. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95.9-96.7% (Herbaspirillum species) and 94.3-95.6% (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6(T) (= NCCB 100033(T) = LMG 21973(T)).

Paulien J. A. Klein Gunnewiek

Papers

Microbial Community Composition Affects Soil Fungistasis

Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

Anti-fungal properties of chitinolytic dune soil bacteria

Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae.

Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil