Call for papers: The Role of Microbial Genomics in Restoration Ecology

Thompson Lake (circa 2009) with the decadent Aphanezomenon blue green pigment of “after bloom”image credit Michael Lemke © Image credit Michael LemkeGuest Edited by Mike Lemke and Rob DeSalle 

For two centuries, microbiologists have recognized that the organisms they study share complex ecological relationships as well as carry out critical roles in the environment. For most of this time, gaining insights to organism identity and relating those to function was a slow process. However, by the end of the 20th century, application of 16S rDNA and metagenomics sequencing (also called environmental or eDNA sequencing) allowed more precise insights to the identity of microorganisms in and on the human body and in natural and unnatural environments. Because of the obvious human health implications, human microbiomes have been a major focus of this technology. With the advance of this technology, researchers also expanded focus to microbial ecology and dynamics of environmentally balanced ecosystems and in contrast, to environmentally damaged systems.

In the mid-20th century, restoration ecology became recognized as field of ecology that focused on reversing the effects of human degradation and destruction of ecosystems.  The process of restoration represents a considerable commitment of time and resources, which are dependent on specific goals and outcomes most often based on historical records.  Sustaining people on this planet and maintaining natural habitats become ever more critical challenges as this century progresses. These endeavors are exasperated by climate change and continued environmental demands forcing resource managers to face the challenge by creating new and differently designed ecosystems (i.e., to perform specific services) or even the creation of novel systems (e.g., systems with native and exotic organisms that arise through human activity).  

A series of valuable questions arise that can be addressed by merging the new technology of eDNA and classical restoration ecology:

Must microbial communities be restored in order to assist efforts to restore the ecosystem?  Does having descriptions of the roles of microorganisms in un-impacted ecosystems enable people to better manage degraded systems? How important is ecosystem structure to help establish microbial function?Is there an assembly of microbial structure that greatly alters the outcome of restoration efforts?  Is an ecosystem microbial flora approach practical for monitoring ecosystem “health”?  Are ecosystem manipulations at the plowing and planting levels, or bulldozer management of vegetation, the equivalent of macro surgery, and while necessary, only part of the approach to establishing ecosystems that are fully functional?  Are microbial transplants and environmental probiotics needed to facilitate management both for function but also to resist disease and propagate macrobiotic as well as microbiotic diversity? Are genetically generated species surveys useful to restoration ecology?

We posit that what the human microbiome has done for medicine, the eDNA approach can do for restoration ecology, including finding and understanding the role of exotic and invasive microbial species in nature.  The purpose of this special edition is to explore the identity, functions, and interactions revealed from the use microbial genomic studies in the study of nature, and to determine how these studies may be applied to better manage degraded systems – and in the end, find what aspects of microbial ecology can be applied to land management practices by conservation experts interested in restoration ecology. We invite submissions to this special issue from authors that can address the variousitemswe list above. We open submissions to papers that address technical, theoretical, analytical and case studies addressing the role of eDNA in restoration ecology.


Guest Editors:

Dr. Mike Lemke is a Full Professor of Biology at the University of Illinois Springfield and is a Research Associate at the American Museum of Natural History, NY.  His research focuses on the microbial ecology of freshwater habitats in Illinois and Brazil large river systems, with special interests in restoration ecology and nutrient dynamics.


Dr. Rob DeSalle, Curator of Molecular Systematics and principle investigator at Sackler Institute for Comparative Genomics at the American Museum of Natural History, NY works in molecular systematics, microbial evolution, and genomics. His current research concerns the development of bioinformatic tools to handle large-scale genomics problems using phylogenetic systematic approaches and focuses on microbial genomics, taxonomy, and systematics.