Steering root microbiomes of a commercial horticultural crop with plant-soil feedbacks

Plant science

Time after time: temporal variation in the effects of grass and forb species on soil bacterial and fungal communities

Microorganisms are found everywhere and have critical roles in most ecosystems, but compared to plants and animals, little is known about their temporal dynamics. Here, we investigated the temporal stability of bacterial and fungal communities in the soil and how their temporal variation varies between grasses and forb species. We established 30 outdoor mesocosms consisting of six plant monocultures and followed microbial communities for an entire year in these soils. We demonstrate that bacterial communities vary greatly over time and that turnover plays an important role in shaping microbial communities. We further show that bacterial communities rapidly shift from one state to another and that this is related to changes in the relative contribution of certain taxa rather than to extinction. Fungal soil communities are more stable over time, and a large part of the variation can be explained by plant species and by whether they are grasses or forbs. Our findings show that the soil bacterial community is shaped by time, while plant group and plant species-specific effects drive soil fungal communities. This has important implications for plant-soil research and highlights that temporal dynamics of soil communities cannot be ignored in studies on plant-soil feedback and microbial community composition and function.Plant science

How plant–soil feedbacks influence the next generation of plants

Plant science

Metagenomic analysis of two important, but difficult to culture, soil-borne bacterial phyla: the Acidobacteria and Verrucomicrobia

Kowalchuk, G.A. [Promotor]Veen, J.A. van [Promotor

Phylogenetic diversity of Acidobacteria in a former agricultural soil

Although Acidobacteria represent the most abundant bacterial phylum in many soils, knowledge of acidobacterial diversity is still rather incomplete. We, therefore, examined the diversity of 16S rRNA genes affiliated with this phylum in a former arable soil via three independent approaches: (1) screening of a fosmid metagenome library for inserts containing Acidobacteria-like 16S rRNA genes; (2) PCR-cloning using general bacterial primers; and (3) PCR-cloning with acidobacterial-specific primers. Bacterial-specific libraries compared rhizosphere versus bulk soil samples, revealing a higher proportion of acidobacterial sequences in bulk soil libraries (P<0.001). Bacterial libraries recovered the greatest diversity, and sequence examination suggested that sequence mismatches with the Acidobacteria-specific primers limited the coverage of the metagenome library screening and specific library approaches. Together, these results expand knowledge of the distribution and diversity of Acidobacteria in soil environments and highlight important technical considerations in the molecular analysis of Acidobacteria diversity.

Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing

Chitin and its derivatives are natural biopolymers that are often used as compounds for the control of soil-borne plant pathogens. In spite of recent advances in agricultural practices involving chitin amendments, the microbial communities in chitin-amended soils remain poorly known. The objectives of this study were (1) to investigate the bacterial diversity and abundance in an agricultural soil supplemented with chitin that turned disease-suppressive and (2) to assess the emergence of chitinolytic bacteria under conditions of raised soil pH. Amplicon pyrosequencing of soil-extracted DNA based on the 16S rRNA genes was used to characterize the structures of bacterial communities in soil, chitin-amended or not, with native versus raised pH (5.7 vs 8.7), in microcosms and the field. As a result of chitin addition, changes in the relative abundances of Actinobacteria, Proteobacteria and Bacteroidetes were observed in the field soil. A large and significant increase of the relative abundance of Oxalobacteraceae (Betaproteobacteria, Burkholderiales) was found. Within the Oxalobacteraceae, the genera Duganella and Massilia showed large increases. Moreover, responses of the Alpha- and Gammaproteobacteria appeared shortly after the alteration of the soil pH in the microcosms. A significant decrease in the abundance of Actinobacteria was observed in the chitin-amended field soil and in the microcosm at high pH. Overall, the bacterial abundance in soil tended to decrease with the addition of chitin. Two groups, Actinobacteria and Oxalobacteraceae, were found to be most responsive to the amendment. These results enhance the understanding of responses to chitin and possible interactions within bacterial communities in soil that can be correlated to soil disease suppressiveness.

MODELING OF NERVOUS SYSTEMS BY DOUBLY STOCHASTIC POISSON PROCESSES

Neuron impulse sequences are represented by doubly stochastic Poisson Processes and Kalman filtering theory is applied to estimate the random intensity functions of the processes. Models of nervous systems in which exitatory and inhibitory synapses have elementary operation, are studied by simultaneous states equations in the theory. The method of estimation is applied to neuron impulse sequences simultaneously recorded from preoptic area of a monkey by a microelectrode

The ecology of Acidobacteria: moving beyond genes and genomes

The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum