BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event.

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event.

Host genomic influence on bacterial composition in the switchgrass rhizosphere.

Host genetic variation can shape the diversity and composition of associated microbiomes, which may reciprocally influence host traits and performance. While the genetic basis of phenotypic diversity of plant populations in nature has been studied, comparatively little research has investigated the genetics of host effects on their associated microbiomes. Switchgrass (Panicum virgatum) is a highly outcrossing, perennial, grass species with substantial locally adaptive diversity across its native North American range.

Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition.

The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS).

The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering.

Fine roots vary dramatically in their functions, which range from resource absorption to within-plant resource transport. These differences should alter resource availability to root-associated microorganisms, yet most root microbiome studies involve fine root homogenization. We hypothesized that microbial filtering would be greatest in the most distal roots.

Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea.

Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer.

Experimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through (i) direct soil transfer at two dilutions and (ii) a new approach, sustained contact between source and recipient soils.

Factoring Ecological, Societal, and Economic Considerations into Inoculant Development.

There are many paths toward effective microbial inoculants for agriculture. Considering what is practical for the present day technological and farming landscape should not limit our creativity in developing innovative technologies. However, factors including production costs, practicality of implementation, and technology adoption by farmers will drive the success of new management approaches.

Microbial lipid biomarkers detected in deep subsurface black shales.

Evidence for microbes has been detected in extreme subsurface environments as deep as 2.5 km with temperatures as high as 90 °C, demonstrating that microbes can adapt and survive extreme environmental conditions. Deep subsurface shales are increasingly exploited for their energy applications, thus characterizing the prevalence and role of microbes in these ecosystems essential for understanding biogeochemical cycles and maximizing production from hydrocarbon-bearing formations.

The Inherent Conflicts in Developing Soil Microbial Inoculants.

Potentially beneficial microorganisms have been inoculated into agricultural soils for years. However, concurrent with sequencing advances and successful manipulation of host-associated microbiomes, industry and academia have recently boosted investments into microbial inoculants, convinced they can increase crop yield and reduce fertilizer and pesticide requirements. The efficacy of soil microbial inoculants remains unreliable, and unlike crop breeding, in which target traits (e.

Corrigendum: Modified Lipid Extraction Methods for Deep Subsurface Shale.

[This corrects the article on p. 1408 in vol. 8, PMID: 28790998.

Modified Lipid Extraction Methods for Deep Subsurface Shale.

Growing interest in the utilization of black shales for hydrocarbon development and environmental applications has spurred investigations of microbial functional diversity in the deep subsurface shale ecosystem. Lipid biomarker analyses including phospholipid fatty acids (PLFAs) and diglyceride fatty acids (DGFAs) represent sensitive tools for estimating biomass and characterizing the diversity of microbial communities. However, complex shale matrix properties create immense challenges for microbial lipid extraction procedures.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing.

Marcellus and mercury: Assessing potential impacts of unconventional natural gas extraction on aquatic ecosystems in northwestern Pennsylvania.

Mercury (Hg) is a persistent element in the environment that has the ability to bioaccumulate and biomagnify up the food chain with potentially harmful effects on ecosystems and human health. Twenty-four streams remotely located in forested watersheds in northwestern PA containing naturally reproducing Salvelinus fontinalis (brook trout), were targeted to gain a better understanding of how Marcellus shale natural gas exploration may be impacting water quality, aquatic biodiversity, and Hg bioaccumulation in aquatic ecosystems. During the summer of 2012, stream water, stream bed sediments, aquatic mosses, macroinvertebrates, crayfish, brook trout, and microbial samples were collected.

Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania.

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured.