The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability

Abstract

Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.

Keywords: Culturing; Environmental sustainability; Genomics; Microbial communities; Restoration ecology; Sample preservation.

Fig. 1

Comparison of cryopreservation methods for microbial assemblages. The percent survival of Bacteria (formerly Eubacteria) (A), Gammaproteobacteria (B), and Betaproteobacteria (C) after cryopreservation. Percent survival is plotted for 10 different cryopreservation methods. The cryopreservation of microbial assemblages was allowed to incubate at − 180 °C for 6 months before slowly thawing and then assessed by culture-dependent and culture-independent techniques. The treatments are as follows: 1, freeze with trehalose; 2, freeze with DMSO; 3, freeze without cryoprotectant (CPA); 4, Mr. Frosty (MF) with trehalose; 5, MF with DMSO; 6, MF without CPA; 7, lyophilize with trehalose; 8, lyophilize with DMSO; 9, lyophilize without CPA; 10, trehalose only immediate analysis; 11, DMSO only with immediate analysis; 12, no method, no CPA with immediate analysis. Treatments 10, 11, and 12 served as controls. Red line indicates 70% survival; the results of the cryopreservation experiments indicate that different phyla react to cryopreservation in varied fashion. (see text) (data from and are available at [110]; used with permission)