Revealing the Ecological Role of Gemmatimonadetes Through Cultivation and Molecular Analysis of Agricultural Soils

Bacteria belonging to phylum Gemmatimonadetes are frequently detected in a variety of environments using culture-independent methods. Despite their ubiquity and prevalence, almost nothing is known about their physiology or ecology because so few strains have been isolated. The first objective of this study was to determine the distribution of Gemmatimonadetes within soil aggregates and the response of the relative abundance of Gemmatimonadetes to dry/wet cycling and soil management. The second objective was to analyze the effects of soil management, aggregate size, and atmospheric conditions on cultivability of Gemmatimonadetes. Universal and Gemmatimonadetes-specific 16S rRNA gene primers were used to determine relative abundance of Gemmatimonadetes in whole soil, macro-, and micro-aggregates. The relative abundance of Gemmatimonadetes was not enriched in the aggregate fractions. Soil subjected to wet/dry cycling had a lower relative abundance of Gemmatimonadetes than control soil at constant moisture. Tillage alone did not affect the distribution of Gemmatimonadetes in the soil. Over 100 putative Gemmatimonedetes isolates were obtained in cultivation experiments. Amongst these, strains Gmat50, Gmat59 and Gmat410, were confirmed to be Gemmatimonadetes via 16S rRNA gene sequencing. Sequence analysis revealed that the 16S rRNA gene of Gmat50 and Gmat410 were 93% and 95% identity, respectively, isolate Ellin5290. The closest cultivated relative of Gmat59 was isolate Ellin7146 with an identity of 88% over the 16S rRNA gene fragment analyzed. Gemmatimonadetes was successfully cultivated under both aeration conditions but was more frequently detected on plates incubated aerobically. Plates inoculated with tilled soil yielded more frequent detection of Gemmatimonadetes than plates inoculated with no-till soil. In conclusion the results indicated that the distribution of Gemmatimonadetes in soil was more dependent on moisture availability than aggregation and suggested members of this phylum are well adapted to low moisture conditions but unable to resist moisture fluctuations induced by wet/dry cycling. Furthermore, cultivability was improved by extended incubation time but not by reduced oxygen concentration and elevated CO2. These results are consistent with a predominantly aerobic niche and homogenous distribution of Gemmatimonadetes at the aggregate scale.