Rumen Archaea Interaction with Volatile Fatty Acids

Abstract

Methane gas is one of the climate changes affecting gases. CH4 emissions from ruminants account for about 81% of methane emissions from the livestock sector, of which 90% are the result of methanogenesis by rumen microbes. As rumen archaea is involved in fermentation process is important to know which of biochemical fermentation parameters it could be related. For this reason, we calculated correlation by using DNA sequencing and fermentation biochemical parameters data from 54 rumen samples. The DNA was isolated from the rumen contents using a solution of phenol, chloroform and isoamyl alcohol. The QIAquick PCR Purification kit (Qiagen, Germany) was used for DNA isolation and purification. Libraries of bacterial 16S ribosomal RNA gene (rRNA) V4 region were prepared following the “16S metagenomic sequencing library preparation” protocol (Illumina), by using 515 F and 806R primers with Illumina adapters. Libraries were sequenced with Illumina MiSeq (Finnish Functional Genomics Centre, Turku) using PE approach and 2 x 250 bp chemistry. Sequencing data were further processed using Qiime v 1.9.1 The pH of a sample of rumen contents was measured immediately after collection using a Twin pH meter (Horiba, Japan). Volatile fatty acid (VFA) levels in rumen contents samples were determined by gas chromatography. Acetic, propionic, isobutyric, butyric, methyl-valeric, valeric, caproic and enanthic levels (mmol/L) were measured in rumen contents. A GC-2010 Plus gas chromatograph (Shimadzu Corp., Kyoto, Japan) with a mass spectrometry detector GCMS-QP2010 (Shimadzu Corp., Kyoto, Japan) was used for VFA analysis. Statistical analyses were calculated using the open-access online software Calypso, Version 8.84. The correlation coefficient (r) was calculated using Pearson. [...].