Microbial diversity in waters, sediments and microbial mats evaluated using fatty acid-based methods

Abstract

The review summarises recent advances towards a greater comprehensive assessment of microbial diversity in aquatic environments using the fatty acid methyl esters and phospholipid fatty acids approaches. These methods are commonly used in microbial ecology because they do not require the culturing of micro-organisms, are quantitative and reproducible and provide valuable information regarding the structure of entire microbial communities. Because some fatty acids are associated with taxonomic and functional groups of micro-organisms, they allow particular groups of micro-organisms to be distinguished. The integration of fatty acid-based methods with stable isotopes, RNA and DNA analyses enhances our knowledge of the role of micro-organisms in global nutrient cycles, functional activity and phylogenetic lineages within microbial communities. Additionally, the analysis of fatty acid profiles enables the shifts in the microbial diversity in pristine and contaminated environments to be monitored. The main objective of this review is to present the use of lipid-based approaches for the characterisation of microbial communities in water columns, sediments and biomats.

Biogeochemistry of fatty acids in a river-dominated Mediterranean ecosystem (Rhône River prodelta, Gulf of Lions, France): Origins and diagenesis

“…Significant amounts of bacteria-specific fatty acids were found at all sites and sediment depths, and indicate the presence of living benthic bacteria or decaying bacterial material. High percentages of monounsaturated fatty acids (16:1ω7 + 18:1ω7, 17 10-24%) suggest high inputs from Proteobacteria (for review see Mrozik et al, 2014), which is consistent with pyrosequencing data showing that OTUs from this phylum dominate in sediments from the prodelta (Fagervold et al, 2014). The branched forms, anteiso-and iso-15:0 (ai15:0 and i15:0), were dominant over their straight chain C 15 homologue.…”

“…Together with 17:0 and 18:1ω9, they are characteristic of the occurrence of Gram-positive bacteria (Mrozik et al, 2014), but branched 15:0 fatty acids may also be abundant in Gram-negative sulfate-reducing bacteria such as Desulfovibrio (Vainshtein et al, 1992). These fatty acids were clustered together with 14:0, suggesting a bacterial source for this non-specific compound, since 14:0 may also be abundant in certain cyanobacteria (Mrozik et al, 2014). This suite of markers were not only found in the offshore stations, but also in the suspended OM delivered by the Rhône River.…”

A diagnostic GDGT signature for the impact of hydrothermal activity on surface deposits at the Southwest Indian Ridge

“…However, these approaches have inherent limitations, such as inconsistent DNA recovery, kinetic biases inherent in polymerase chain reaction, and the need to develop sepecific and appropriate primers and probes (Chowdhury and Dick, 2012). Organic geochemical approaches also have limitations but can offer a complementary view on microbial community structures since they do not require the culturing of microorganisms, are quantitative and reproducible, and can integrate a longer time window than nucleic acid based researches (Mrozik et al, 2014). There has been some research on lipid biomarkers in hydrothermal fluids, sulfides, oxides, hydrothermally heated sediments and organisms from the Mid-Atlantic Ridge, Arctic Mid-Ocean Ridge, East Pacific Rise, Guyamas Basin spreading center and other hydrothermal systems (e.g.…”

Study of Correlation between Milk Yield and Intestinal Microbes in Chinese Holstein Cows under the Same Diet

“…In this study, based on homologous sequence alignment method and clustering with information extracted from RDF and BLAST databases, the unique representative sequence reads were obtained, which were delimited for further analysis (as the Table 2 showed 21,230,11,424,30,526,25,666,16,686, and 14,032 effective reads of the CHC1, CHC2, CHC3, CHC4, CHC5 and CHC6). Using the software program Mothur and sequence identity criteria cut off of 97%, these sequences were assigned to some Operational taxonomic units (OTUs).…”

“…With the development of DNA sequencing technology, researchers have focused on the cultureindependent metagenomic approaches, using either a sequence-based or a functional-based application [15]. Over the past two decades, the field of environmental ecology has made tremendous progress, and a wide variety of methods using signature lipid biomarkers and nucleic acids have been developed to describe and characterize the functional and phylogenetic diversity of microorganisms [16]. The advent of The fresh feces were obtained from these Holstein cows rectums which were fed the same fodder.…”