Microbial assemblages and bioindicators as proxies for ecosystem health status: potential and limitations

被引:65
作者
Astudillo-Garcia, Carmen [1 ]
Hermans, Syrie M. [1 ]
Stevenson, Bryan [2 ]
Buckley, Hannah L. [3 ]
Lear, Gavin [1 ]
机构
[1] Univ Auckland, Sch Biol Sci, 3A Symonds St, Auckland 1010, New Zealand
[2] Manaaki Whenua Landcare Res, Private Bag 3127, Hamilton 3240, New Zealand
[3] Auckland Univ Technol, Sch Sci, 55 Wellesley St East, Auckland 1010, New Zealand
关键词
Microbial indicators; Ecosystem health; Molecular; Statistics; BACTERIAL COMMUNITY RESPONSE; LONG-TERM; MERCURY RESISTANCE; METAL RESISTANCE; GUT BACTERIA; FRESH-WATER; DIVERSITY; SOIL; INDICATOR; SEDIMENTS;
D O I
10.1007/s00253-019-09963-0
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Microorganisms play fundamental roles in the diversity and functional stability of environments, including nutrient and energy cycling. However, microbial biodiversity loss and change because of global climate and land use change remain poorly understood. Many microbial taxa exhibit fast growth rates and are highly sensitive to environmental change. This suggests they have potential to be efficient biological indicators to assess and monitor the state of the habitats within which they occur. Here, we describe and illustrate a range of univariate and multivariate statistical approaches that can be used to identify effective microbial indicators of environmental perturbations and quantify changes in microbial communities. We show that the integration of multiple approaches, such as linear discriminant analysis effect size and indicator value analysis, is optimal for the quantification of the effects of perturbation on microbial communities. We demonstrate the most prevalent techniques using microbial community data derived from soils under different land uses. We discuss the limitations to the development and use of microbial bioindicators and identify future research directions, such as the creation of reliable, standardised reference databases to provide baseline metrics that are indicative of healthy microbial communities. If reliable and globally-relevant microbial indicators of environmental health can be developed, there is enormous potential for their use, both as a standalone monitoring tool and via their integration with existing physical, chemical and biological measures of environmental health.
引用
收藏
页码:6407 / 6421
页数:15
相关论文
共 140 条
[1]   The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update [J].
Afgan, Enis ;
Baker, Dannon ;
Batut, Berenice ;
van den Beek, Marius ;
Bouvier, Dave ;
Cech, Martin ;
Chilton, John ;
Clements, Dave ;
Coraor, Nate ;
Gruening, Bjoern A. ;
Guerler, Aysam ;
Hillman-Jackson, Jennifer ;
Hiltemann, Saskia ;
Jalili, Vahid ;
Rasche, Helena ;
Soranzo, Nicola ;
Goecks, Jeremy ;
Taylor, James ;
Nekrutenko, Anton ;
Blankenberg, Daniel .
NUCLEIC ACIDS RESEARCH, 2018, 46 (W1) :W537-W544
[2]   A real-time polymerase chain reaction assay for quantitative detection of the human-specific enterococci surface protein marker in sewage and environmental waters [J].
Ahmed, W. ;
Stewart, J. ;
Gardner, T. ;
Powell, D. .
ENVIRONMENTAL MICROBIOLOGY, 2008, 10 (12) :3255-3264
[3]   Three common metal contaminants of urban runoff (Zn, Cu & Pb) accumulate in freshwater biofilm and modify embedded bacterial communities [J].
Ancion, Pierre-Yves ;
Lear, Gavin ;
Lewis, Gillian D. .
ENVIRONMENTAL POLLUTION, 2010, 158 (08) :2738-2745
[4]  
Anderson MJ, 2003, ECOLOGY, V84, P511, DOI 10.1890/0012-9658(2003)084[0511:CAOPCA]2.0.CO
[5]  
2
[6]  
Anderson MJ, 2001, AUSTRAL ECOL, V26, P32, DOI 10.1111/j.1442-9993.2001.01070.pp.x
[7]  
[Anonymous], 2006, PRIMER v6
[8]  
[Anonymous], ENV RES I REP
[9]  
[Anonymous], ENV MONIT ASSESS
[10]  
[Anonymous], 2002, 388 NAT ENV RES I RO