The Family Micrococcaceae

Dastager, Syed G.; Krishnamurthi, Srinivasan; Rameshkumar, N.; Dharne, Mahesh

doi:10.1007/978-3-642-30138-4_168

Cited by 23 publications

(22 citation statements)

References 228 publications

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“…The families that were more prevalent in media without antibiotics include the Micrococcaceae, Burkholderiaceae, and Moraxellaceae. Members of the Micrococcaceae and Burkholderiaceae are metabolically flexible (Coenye, 2014;Dastager et al, 2014), and the cultured Moraxellaceae belong to nonfastidious members of this bacterial family (Teixeira & Merquior, 2014). All the families dominant in samples without antibiotics therefore have flexible metabolic strategies and higher growth rates -i.e., they are r-strategists.…”

Section: Discussionmentioning

confidence: 99%

The impact of sample processing and media chemistry on the culturable diversity of bacteria isolated from a cave

Bender¹,

Glover²,

Archey³

et al. 2020

IJS

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Although molecular approaches can identify members of microbial communities in the environment, genomic information does not necessarily correlate with environmental phenotype. Understanding functional roles can be done by cultivating representative species, yet the culturablility of bacteria from caves remains low, at 0.02%, limiting our understanding of microbial community interactions and processes. We have investigated several factors influencing culturability of bacteria from a single sample location in Maxwelton Sink Cave, WV, USA. Extended incubation of inoculated plates showed a significant increase in colony counts from two to four weeks, indicating that extended incubations increase culturability. There were no significant differences in plate counts or diversity measures when the sample was suspended in different buffers prior to cultivation, while samples plated immediately after collection demonstrated higher culturability. Although supplementing the media with antibiotics reduced colony counts and cultured diversity, these plates did appear to contain a higher proportion of slow-growing oligotrophs. Finally, among a selection of culture media used, pyruvate agar showed the highest culturability and bacterial diversity, which may be a result of the oxygen radical scavenging effects of pyruvate. By identifying methods that improve culturable diversity, we hope to further understand the roles played by bacteria in cave communities, and test hypotheses that are best assessed using culture-based methods, such as screening for bioactive compounds or confirming in situ metabolic strategies.

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Section: Discussionmentioning

confidence: 99%

The impact of sample processing and media chemistry on the culturable diversity of bacteria isolated from a cave

Bender¹,

Glover²,

Archey³

et al. 2020

IJS

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“…However, the 16S rRNA data in this study revealed that the phylum Actinobacteria was the most important. Its prevalent potentially active members, including those in the families Intrasporangiaceae (22.5%), Micrococcaceae (19.0%) and Nocardiaceae (12.3%) ( S6 Table ), were all reported to include increasing number of human-related pathogens [ 59 – 61 ].…”

Section: Discussionmentioning

confidence: 99%

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

et al. 2017

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RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5’ adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10–100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples.

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“…Some notable examples within the families Streptococcaceae , Staphylococcaceae , Micrococcaceae , and Corynebacteriaceae can be human skin–associated taxa, which supports the idea that these contaminants are introduced by researchers as they prepared the samplers. 42–45 However, OTUs from the families Sphingomonadaceae , Xanthomonadaceae , and Rhodobacteraceae , which are typically of environmental origin, were also in these categories. 46–48 To be conservative, the OTUs in Categories B and C should also be removed from the data set because they are known to be at least equally prevalent in the closed sampler as in the open sampler.…”

Section: Resultsmentioning

confidence: 99%

A Method for Collecting Atmospheric Microbial Samples From Set Altitudes for Use With Next-Generation Sequencing Techniques to Characterize Communities

Spring

Docherty

Domingue

et al. 2018

Air, Soil and Water Research

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Dispersal of airborne microorganisms is an important ecological process, resulting in the distribution of bacteria to all habitats on Earth. Investigation of this process is limited by the ability to collect uncontaminated high-altitude microbial samples for use with next-generation sequencing approaches. Here, we describe the design of a Remote Airborne Microbial Passive sampling system. Troubleshooting experiments demonstrate that the samplers collect adequate DNA for bacterial 16S rRNA (ribosomal RNA) amplicon-based Mi-Seq sequencing at 2 and 150 m from the ground. When samplers are closed, they retain only a low number of sequences, and may be used as a negative control. We also demonstrate that the optimal amount of collection dishes to include in the sampler is 8, and that freezing collection dishes at −80°C is an alternative to immediate DNA extraction. Samplers may be used to address a variety of ecological and human health-related questions.

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The Family Micrococcaceae

Cited by 23 publications

References 228 publications

The impact of sample processing and media chemistry on the culturable diversity of bacteria isolated from a cave

The impact of sample processing and media chemistry on the culturable diversity of bacteria isolated from a cave

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

A Method for Collecting Atmospheric Microbial Samples From Set Altitudes for Use With Next-Generation Sequencing Techniques to Characterize Communities

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