Phospholipid fatty acid profiling of microbial communities-a review of interpretations and recent applications

Willers, Clarissa; Rensburg, Peet Jansen van; Claassens, Sarina

doi:10.1111/jam.12902

Cited by 300 publications

(232 citation statements)

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“…Cis and trans geometry are indicated by the suffixes c and t. The branching is indicated as iso or anteiso, 10Me indicates a methyl group on the tenth carbon atom from the carboxyl end of the molecule, position of hydroxyl (OH) groups is noted, and cyclo indicates cyclopropane fatty acids. The lipid biomarker PLFAs used to represent the different microbial groups are as follows: C14:0, C15:0, C16:0, C17:0 and C18:0 for general bacterial; i14:0, i15:0, a15:0, a16:0, i17:0, a17:0, a18:0 for G + bacteria; 16:1 2OH, 16:1w7c, 16:1w9c, 16:1w9t, 17:1w8c, Cyclo 17:0, 18:1w5c, 18:1w7c, 18:1w9t, and Cyclo 19:0 for G − bacteria; 10Me16:0, 10Me17:0 and 10Me18:0 for actenomycetes and 16:1w5c, 18:1w9c, 18:3 w6c and 18:2 w9c for fungi30. All the PLFA biomarkers mentioned above were considered representative of total PLFA of soil microbial community.…”

Section: Methodsmentioning

confidence: 99%

“…All the PLFA biomarkers mentioned above were considered representative of total PLFA of soil microbial community. Ratio of F to B, G − to G + , sat to unsat, trans to cis were used as indicator of shifts of microbial community structure30.…”

Section: Methodsmentioning

confidence: 99%

“…The changes in specific marker PLFAs in PLFA profiles described the changes of specific group as well as overall structure of microbial communities29. Furthermore, changes the ratios of sat/monouns, fungi/bacteria, G + /G − , iso/anteiso and trans/cis PLFAs can be used to described changes of community structure2930. Therefore, we used PLFA technique to study the changes in specific PLFA markers representative of specific microbial groups to describe influence of different doses of N-fertilizer and P. liquidambari on community structure of rhizosphere soil of rice.…”

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confidence: 99%

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Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

Siddikee

Zereen

et al. 2016

Sci Rep

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Microbial community structure and functions of rhizosphere soil of rice were investigated after applying low and high doses of nitrogenous fertilizer and Phomopsis liquidambari. Average well color development, substrate richness, catabolic diversity and soil enzymes activities varied after applying N-fertilizer and P. liquidambari and were greater in P. liquidambari treated soil than only N-fertilization. Multivariate analysis distinctly separated the catabolic and enzymes activity profile which statistically proved alteration of microbial functional diversity. Nitrogen fertilizer altered microbial community structure revealed by the increased content of total PLFAs, specific subgroup marker PLFAs except fungal PLFAs and by the decreased ratio of G + /G− , sat/monunsat, iso/anteiso, F/B except trans/cis while P. liquidambari inoculation enhanced N-fertilization effect except increased fungal PLFA and decreased trans/cis. PCA using identified marker PLFAs revealed definite discrimination among the treatments which further statistically confirmed structural changed of microbial community. Nitrogenase activity representative of N-fixing community decreased in N-fertilizer treatment while P. liquidambari inoculation increased. In short, application of P. liquidambari with low doses of N-fertilizer improved rice growth and reduced N-fertilizer requirement by increasing enzymes activities involved in C, N and P cycling, structural and functional diversity of microbes, nitrogenase activity involved in N 2 fixation and accumulation of total-N.Rice (Oryza sativa L.) is the second largest crop in terms of planted area and yield in the world. The cultivation of rice gives rise to anoxic conditions in growing season but aerobic conditions during non-growing season 1 . Thus, composition and structure of microbial community in rice field are diverse and very complicated 2 . Agricultural management practices, particularly inputs of fertilizers and manure, tillage, cover crops, cropping system and season, soil pH and application of plant growth promoting bacteria or fungi have large impacts on the size and activity of soil microbial communities [3][4][5][6][7][8] . Nitrogen is the top most important macronutrients and limiting factor for plant growth and development 9 . Soils are routinely fertilized to overcome N-limitation and maximize crop yield. But, repeated fertilizer applications change soil physical, chemical and biological properties consequently directly or indirectly influence the growth and activity of certain group of microbes and adaptation ability of different groups of microbes varies with nutritional status 10,11 . The rhizosphere of plant itself is also a unique ecological niche and shapes the structure of microbial community by releasing specific substrates or by the specific physical, chemical and biotic environment created by the plant root in terms of O 2 , pH etc. 12,13 . Quality and quantity of root exudates depends on plant species, nutrient levels, biotic and abiotic stresses and colonization by PGP mi...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

Siddikee

Zereen

et al. 2016

Sci Rep

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“…Even though the PLFA signature method is not as advanced as genomic technology, it has been used extensively with good results to analyze the biomass and structures of microbial communities (Frostegård et al, 2011). Bacteria, including Gram-positive (G + ) and negative (G − ) bacteria, generally degrade labile compounds by excreting hydrolase, while fungi, including arbuscular mycorrhizal fungi (AMF) and saprophytes (SAP), are responsible for degrading recalcitrant compounds by secreting oxidase (Burns et al, 2013;Sinsabaugh et al, 2010;Willers et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China

Zhang

Zou

et al. 2017

Biogeosciences

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Abstract. The nitrate to ammonium ratios in nitrogen (N) compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH 4 Cl) and nitrate (NaNO 3 ) at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH 4 Cl) and nitrate (NaNO 3 ) applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs) decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G + ) and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF) PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP) than ammonium. The activities of Nacquisition specific enzymes (enzyme activities normalized by total PLFA contents) were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA), we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO) activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate

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“…() and the profiling of soil microbial community was based on guidelines provided by Willers et al. () and Tavi et al. ().…”

Section: Methodsmentioning

confidence: 99%

Impact of fertilization on cover crops and microbial community on a bauxite‐mined soil undergoing reclamation

Teixeira

Souza

Santos

et al. 2019

J. Plant Nutr. Soil Sci.

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The reclamation of bauxite‐mined areas can be favored by the application of organic and/or chemical fertilization to restore the vegetation. Otherwise, the impact of fertilizations on soil microbiota or plant–microbe interactions as land reclamation progresses is less understood. To address this issue, we evaluated the impact of organic and chemical fertilization on plants and soil microbial community within the first 36 months of land reclamation in a bauxite‐mined site. The experiment was set up according to a split‐plot design in which the main plots received fertilizations [non‐fertilized control (NF), chemical fertilization (CF; NPK and rock phosphate), organic fertilization (OF; poultry litter), and CF+OF combined], and the subplots received cover crops [no cover crops (NC), grass (B; Brachiaria), legume (S, Stylosanthes), and B+S combined]. Cover crops biomass yield was assessed annually with five field campaigns per year. We used phospholipid fatty acids (PLFAs) to infer the impacts of mining and restoration practices on actinobacteria, Gram‐negative and Gram‐positive bacteria, arbuscular mycorrhizal fungi, and fungi. Accordingly, PLFAs were determined before bauxite mining (pre‐mining), six months after topsoil reconfiguration (post‐mining), and after 14 and 36 months following the application of the fertilizations and cover crops. PLFAs results indicated that in post‐mining, the living microbiota was significantly lower than in pre‐mining. Cover crops biomass yield was highest for B and B+S fertilized with CF+OF at 14 and 36 months. Both parametric and non‐parametric statistics showed a temporal variation in the response of living microbes to the treatments applied. After 14 months, living microbes showed greatest response to OF, while at 36 months their response was strongest in the treatments with highest plant biomass production (B and B+S). These results suggest that in the early stages of land reclamation, living microbial biomass benefit the most from organic fertilizers. As this initial boost decline, living microbes are more likely to thrive in areas undergoing reclamation where they can develop synergistic interactions with plants.

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Phospholipid fatty acid profiling of microbial communities-a review of interpretations and recent applications

Cited by 300 publications

References 124 publications

Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China

Impact of fertilization on cover crops and microbial community on a bauxite‐mined soil undergoing reclamation

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