Determining replication for discrimination among microbial communities in environmental samples using community-level physiological profiles

Lowit, M.B; Blum, Linda K.; Mills, Aaron L.

doi:10.1111/j.1574-6941.2000.tb00703.x

Cited by 11 publications

(7 citation statements)

References 24 publications

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“…Water samples were collected in 50-mL, sterile, plastic, centrifuge tubes and immediately capped. All ponds were sampled in 30 min or less, and each sample was directly inoculated into the 96 microwells (150 L of sample per well) of the EcoPlate within 30 min of collection (Lowit et al 2000;Preston-Mafham et al 2002) with an eight-channel pipettor. EcoPlates were incubated at 21 ± 2 • C in the dark (Christian and Lind 2006) for a maximum of 224 h or until AWCD ≥ 1 (Weber and Legge 2010).…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Community‐Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds

Kurten

Barkoh

2015

N American J Aquac

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Microbial communities in aquaculture ponds play pivotal roles in pond productivity and fish production success. Nonetheless, culturists do not consider this variable in pond management decision making likely because of a lack of practical assessment tools. Therefore, we evaluated the community-level physiological profiling (CLPP) technique for characterizing microbial community function for use in aquaculture. Unfiltered water samples collected from various plastic-lined ponds over time were incubated on Biolog EcoPlates. Responses (substrate optical densities) were measured at 24-h intervals for up to 12 d to determine the best incubation interval and the number of required replicates needed for determining microbial community function in aquaculture ponds. The repeatability and withinpond variability of the CLPP metrics were also evaluated. During cooler months and in ponds with no fish and low apparent microbial activity, a 96-h incubation period was required to differentiate microbial community functional characteristics. During warmer months and when ponds were stocked with fish and had significant phytoplankton blooms, incubation periods of 72 h were sufficient. For routine monitoring, a single sample of pond water on one Biolog EcoPlate was adequate for assessing microbial community function. Multiple water samples from a single pond revealed low heterogeneity in the microbial community function. When multiple Biolog EcoPlates were inoculated with a single sample of pond water the dissimilarity of substrate responses was low (2.9%), indicating high repeatability of the CLPP technique. The CLPP method appears to be robust and allows for the assessment of functional characteristics of the heterotrophic microbial community such as relative diversity, similarity, and community functional activity. Therefore, this technique may be used by fish culturists to assess hatchery pond microbial community function, which would lead to a better understanding of the importance of the microbial community to the overall aquaculture pond ecosystem function. Such a tool would allow improved and more comprehensive management of aquaculture pond ecosystems.

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Section: Methodsmentioning

confidence: 99%

Evaluation of Community‐Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds

Kurten

Barkoh

2015

N American J Aquac

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“…The application of Biolog microplates for microbial community analysis has several indispensable problems [15]. Among the criticisms was the lack of replication and statistical weakness [16]. An alternative to Biolog microplates, the Biolog EcoPlates can analyze 31 substrates that were selected from past environmental applications and arranged on the three blocks in a single microplate for triplicate analyses; these EcoPlates potentially have great merit for microbial community level physiological profiling and have been used to assess functional diversity among various environments [15].…”

Section: Introductionmentioning

confidence: 99%

Shifts of Bacterioplankton Metabolic Profiles along the Salinity Gradient in a Subtropical Estuary

et al. 2013

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Understanding the biodegradation potential of river bacterioplankton communities is crucial for watershed management. We investigated the shifts in bacterioplankton metabolic profiles along the salinity gradient of the Caloosahatchee River Estuary, Florida. The carbon source utilization patterns of river bacterioplankton communities were determined by using Biolog EcoPlates. The number of utilized substrates was generally high in the upstream freshwater dominated zone and low in the downstream zone, suggesting a shift in metabolic profiles among bacterioplankton assemblages along the estuarine gradient. The prokaryotic cell numbers also decreased along the estuarine salinity gradient. Seasonal and site-specific differences were found in the numbers of utilized substrates, which were similar in summer and fall (wet season) and winter and spring (dry season). Bacterioplankton assemblages in summer and fall showed more versatile substrate utilization patterns than those of winter and spring communities. Therefore, our data suggest that microbial metabolic patterns in the subtropical estuary are likely influenced by the water discharge patterns created by dry and wet seasons along the salinity gradient.

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“…Negative values were set to zero. The data were normalized (scaled) by dividing each OD value by the AWCD [15,17], and the adjusted OD values were used for statistical analysis.…”

Section: Discussionmentioning

confidence: 99%

“…In the present study, we used the original concept of data analysis (AWCD scaling) suggested by Garland and Mills [15]. This concept has been critically discussed [26,27], but recent evaluations of data handling support the usefulness of the method [17,23].…”

Section: Effects On Functional Diversitymentioning

confidence: 99%

Effects of linear alkylbenzene sulfonates on functional diversity of microbial communities in soil

Vinther

Mortensen

Elsgaard

2003

Enviro Toxic and Chemistry

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Linear alkylbenzene sulfonates (LAS) often occur in sewage sludge that is applied to agricultural soil. Here LAS may affect the microbial activity, which is an important basis for nutrient cycling. Previous studies have shown that single bacterial species and specific soil processes can be very sensitive to LAS. Here we report that two levels of LAS, 22 and 174 mg/kg dry weight soil, had little or no significant influence of the functional diversity of bacteria in a sandy soil, as tested by community-level physiological profiles. Briefly, these profiles are a characterization of the microbial communities based on the pattern of substrate utilization in 96-well microtiter plates (Biolog EcoPlates). Sandy agricultural soil was incubated in duplicate 1-L mesocosms with or without LAS, and bacteria were extracted after one, two, and four weeks. During incubation, more than 98 and 93% of LAS added to 22 and 174 mg/kg dry weight soil was degraded, respectively. The presence of LAS at 174 mg/kg dry weight caused a higher number of bacteria in the soil extracts, maximally corresponding to 2.5 times the numbers in LAS-free soil (1.8 x 10(7) cells/g dry wt soil) after four weeks of incubation. No inhibitory effect of LAS was observed when the substrate utilization data were analyzed for substrate richness and diversity (Shannon-Weaver indices). Principal component analysis, however, showed that the pattern of substrate utilization in soil with the highest LAS content (174 mg/kg dry wt) could be distinguished from control soil and soil with 22 mg LAS/kg dry weight. Yet the overall conclusion was that the functional diversity of the aerobic, heterotrophic bacterial community was rather insensitive to LAS.

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Determining replication for discrimination among microbial communities in environmental samples using community-level physiological profiles

Cited by 11 publications

References 24 publications

Evaluation of Community‐Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds

Evaluation of Community‐Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds

Shifts of Bacterioplankton Metabolic Profiles along the Salinity Gradient in a Subtropical Estuary

Effects of linear alkylbenzene sulfonates on functional diversity of microbial communities in soil

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