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While the composition of these ecosystems can serve as baselines for future study, the interactions that researchers uncover when examining microbial community ecology are also important. They saw a need to encourage people to move into the next, next generation of microbial ecology (first generation microbial ecology was what the authors were "raised on" - culture plates, biochemistry, and an introduction to molecular and was built on pre-generation microbial ecology being all that came before, moving to the current, next-generation microbial ecology, which is what we are doing now and which incorporates next-generation sequencing [NGS]. The significantly more diverse meadow ecosystem was like diversity in the restored urban and suburban ecologies. c. B I Agriculture i b - The human practice of agriculture is an inherently disruptive process with regard to natural ecosystems. While this Special Issue (SI) entitled I The Role of Microbial Genomics in Restoration Ecology i does not claim to be an exhaustive review of current work spanning microbial ecology, restoration ecology, and genomics, the 25 manuscripts we have assembled for this issue represent a wide cross-section of current work being done on the topic. [Extracted from the article]

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. [ABSTRACT FROM AUTHOR]

Are we moving to a world where ecosystem restoration plans are assembled around the aquatic and terrestrial microorganisms first, given their importance, then building in the plants and animals? In the mid-twentieth century, restoration ecology became recognized as a field of ecology that focused on reversing the effects of human degradation and destruction of ecosystems. Welcome to this Special Issue of Microbial Ecology that explores the role of microbial genomics in restoration ecology. [Extracted from the article]

With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four flood-pulsed systems (Amazon [ n = 21], Araguaia [ n = 14], Paraná [ n = 15], and Pantanal [ n = 8]) in 2011-2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes. We report here a global comparison of the bacterioplankton makeup of freshwater systems, focusing on a comparison of Brazilian lakes with similar freshwater systems across the globe. The results indicate a surprising similarity at higher taxonomic levels of the bacterioplankton in Brazilian freshwater with global sites. However, substantial novel diversity at the family level was also observed for the Brazilian freshwater systems. Brazilian freshwater bacterioplankton richness was relatively average globally. Ordination results indicate that Brazilian bacterioplankton composition is unique from other areas of the globe. Using Brazil-only ordinations, floodplain system differentiation most strongly correlated with dissolved oxygen, pH, and phosphate. Our data on Brazilian freshwater systems in combination with analysis of a collection of freshwater environmental samples from across the globe offers the first regional picture of bacterioplankton diversity in these important freshwater systems. [ABSTRACT FROM AUTHOR]

Bacteria were identified from a large, seasonally flooded river (Paraná River, Brazil) and two floodplain habitats that were part of the same river system yet very different in nature: clearwater Garças Lagoon and the highly humic waters of Patos Lagoon. Bacterioplankton were collected during mid-summer (Jan. 2002) from water samples (2 l) filtered first through a 1.2-μm filter then a 0.2-μm membrane filter representing the particle-attached and free-living sub-communities, respectively. DNA was extracted from filters and purified and a 16S rRNA clone library established for each habitat. Over 300 clones were sequenced and checked for similarity to existing 16S sequences in GenBank using the BLAST algorithm with default parameters. Further classification of clones was done using a species “backbone” attachment followed by parsimony analysis. The majority (85%) of sequences, referred to here as operational taxonomic units (OTUs), were most similar to uncultured bacterium 16S sequences. OTUs from each Proteobacteria sub-phylum ( α, β, γ, δ, ɛ) were present in the Upper Paraná River system, as well as members of the Bacteroidetes. The microbial assemblage from Patos Lagoon was least like other samples in that it had no Firmicutes present and was dominated by Actinobacteria. Verrucomicrobia OTUs were only found in the free-living assemblage. This study documents the presence of globally distributed phyla in Upper Paraná River and taxa unique to habitat and particle attachment. [ABSTRACT FROM AUTHOR]