Significant interest exists in engineering the soil microbiome to attain suppression of soil-borne plant diseases. Anaerobic soil disinfestation (ASD) has potential as a biologically regulated disease control method; however, the role of specific metabolites and microbial community dynamics contributing to ASD mediated disease control is mostly uncharacterized. Understanding the trajectory of co-evolutionary processes leading to syntrophic generation of functional metabolites during ASD is a necessary prelude to the predictive utilization of this disease management approach. Consequently, metabolic and microbial community profiling were used to generate highly dimensional datasets and network analysis to identify sequential transformations through aerobic, facultatively anaerobic, and anaerobic soil phases of the ASD process and distinct groups of metabolites and microorganisms linked with those stages. Transient alterations in abundance of specific microbial groups, not consistently accounted for in previous studies of the ASD process, were documented in this time-course study. Such events initially were associated with increases and subsequent diminution in highly labile metabolites conferred by the carbon input. Proliferation and dynamic compositional changes in the Firmicutes community continued throughout the anaerobic phase and was linked to temporal changes in metabolite abundance including accumulation of small chain organic acids, methyl sulfide compounds, hydrocarbons, and p-cresol with antimicrobial properties. Novel potential modes of disease control during ASD were identified and the importance of the amendment and “community metabolism” for temporally supplying specific classes of labile compounds were revealed.

The bacterial and archaeal communities of the sediments at the base of the Florida Escarpment (Gulf of Mexico, USA) were investigated using molecular phylogenetic analysis. The total microbial community DNA of each of three vertical zones (top, middle and bottom) of a sediment core was extracted and the 16S rRNA genes were amplified by PCR, cloned and sequenced. Shannon-Weaver Diversity measures of bacteria were high in all three zones. For the archaea, diversity was generally low, but increased with depth. The archaeal clonal libraries were dominated by representatives of four groups of organisms involved in the anaerobic oxidation of methane (ANME groups). Phylogenetic analysis of bacteria suggests the dominance of epsilon-proteobacteria in the top zone, the epsilon-, delta- and gamma-proteobacteria in the middle zone and the delta-proteobacteria in the bottom zone of the core. Members of the Cytophaga-Flexibacter-Bacteroidetes group, the Chloroflexi/green non-sulfur bacteria, the Gram+ (Firmicutes), the Planctomyces, candidate division WS3 and Fusobacterium were also detected. Our data suggest that the community structure and diversity of microorganisms can shift greatly within small vertical distances, possibly in response to changes in the physical and chemical conditions.

In April 1991, submarine volcanic eruptions initiated the formation of numerous hydrothermal vents between 9°45# and 9°52#N along the crest of the East Pacific Rise (EPR). Dramatic changes in biological community structure and vent fluid chemistry have been documented throughout this region since the eruptive event. By April 2004, mussels (Bathymodiolus thermophilus) dominated the faunal assemblages at several of the vent sites formed during of after the 1991 eruptions, whereas other habitats within the region were dominated by the vestimentiferan Riftia pachyptila. In the present paper, we build upon the extensive data sets obtained at these sites over the past decade and describe a manipulative experiment (conducted at 9°49.94#N; 104°14.43#W on the EPR) designed to assess interrelationships between vent fluid chemistry, temperature, biological community structure, and seismic activity. To this end, in situ voltammetric systems and thermal probes were used to measure H 2 S/HSand temperature over time in a denuded region of an extensive mussel bed in which an exclusion cage was placed to inhibit the subsequent migration of mussels into the denuded area. Fluid samples were taken from the same locations to characterize the associated microbial constituents. Basalt blocks, which were placed in the cage in April 2004 and subsequently recovered in April 2005, were colonized by more than 25 different species of invertebrates, including numerous vestimentiferans and remarkably few mussels. Recorded temporal changes in vent fluid chemistry and temperature regimes, when coupled with microbiological characterization of the vent fluids and seismic activity data obtained from ocean bottom seismometers, shed considerable light on factors controlling biological community structure in these hydrothermal ecosystems.