Municipal Solid Waste Landfills Harbor Distinct Microbiomes

Abstract

Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

The Metabolic Capability and Phylogenetic Diversity of Mono Lake During a Bloom of the Eukaryotic Phototroph Picocystis strain ML

“…Reactions were purified using AmpureXP paramagnetic beads (Beckman Coulter Inc., Indianapolis, IN) at a final concentration of 0.8 x v/v. After purification, 4 μL of PCR product was used in a barcoding reaction, cleaned, concentrated, and pooled in equimolar amounts as previously described (31). The pooled, prepared library was then submitted for sequencing on the Illumina MiSeq platform (Illumina Inc., San Diego, CA) using V2 PE250 chemistry.…”

Fresh Snowfall Microbiology and Chemistry are Driven by Geography in Storm-Tracked Events

“…Initial sample 16S/18S rRNA PCR amplification was performed in duplicate 25 μL reactions as follows: 1x QuantaBio 5PRIME HotMasterMix, 0.2 μM 515-Y Forward Primer (5’- GTA AAA CGA CGG CCA GT CCG TGY CAG CMG CCG CGG TAA-3’) where the M13 forward primer (underlined) is ligated to the small sub-unit RNA (ssuRNA) specific sequence via a ‘CC’ spacer, 0.2 μM 926R (5’-CCG YCA ATT YMT TTR AGT TT-3’) Reverse Primer and template DNA. Reverse primers were as reported by Parada et al (2015) (32) while forward primers were adapted from Parada et al with the addition of the M13 sequence, as done by Stamps et al (2016) (33). Primers from Parada et al target all three domains of life (32).…”

“…A second, 6 cycle, PCR amplification step with the parameters used in the first amplification step was used to ligate barcodes adapted from Caparaso et. al (2012) (34) to the M13 region of the forward primer (33). PCR product cleanup was performed with 0.8x concentration of KAPA Pure Beads (Kapa Biosystems, Indianapolis, IN) according to the manufacturer’s specifications.…”

Understanding the Anthropocene through the lens of landfill microbiomes

“…) and landfills (Stamps et al . ). Intensive research in relatively “old” landfills is needed to assess the chemical and physical compositions of these sites, as well as for microbial sampling and analysis.…”

“…For instance, recent work focusing on the microbiomes of leachates from 19 non‐hazardous landfills highlighted the potential that microbiomes have as anthropogenic markers (Stamps et al . ). Profiling may initially focus on 16S rRNA gene sequencing along with metagenomic and metatranscriptomic data before advanced mechanistic questions are addressed.…”