Untangling the dynamics of persistence and colonization in microbial communities

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota

Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.

Assessing multiple threats to seabird populations using flesh-footed shearwaters Ardenna carneipes on Lord Howe Island, Australia as case study

Globally, seabird populations have been in decline due to multiple threats throughout their range. Separating simultaneous pressures is challenging and can require significant amounts of data over long periods of time. We use spatial contrasts to investigate the relative importance of several drivers for the purported decline in a species listed as in decline as an example species, the Flesh-footed shearwater (Ardenna carneipes). On Lord Howe Island in the Tasman Sea, Australia, this seabird suffers from habitat loss due to housing development, intensive mortality in fisheries, plastic ingestion, and roadkill due to vehicular traffic on its breeding island. We repeated a quantitative survey of the population to ascertain whether the decline previously reported had continued and to evaluate the purported mortality sources (Reid et al. in PLoS ONE 8(4):e58230, 2013, Lavers et al. in Global Ecol Conserv 17:e00579, 2019). We measured burrow density, area of occurrence, occupancy and breeding success, integrating them with previous surveys using a Bayesian statistical model to generate longer term estimates of demographic rates. We used spatial patterns to test whether mortality on roads or proximity to human habitation was influencing population demographics. In contrast to predictions, we found the population had stabilised or increased. Characteristics such as burrow occupancy and breeding success showed little pattern, with weak evidence for impacts from road mortality and housing development. Such a data-rich approach is substantially more informative and can better support seabird conservation and management efforts does require more field-time and additional equipment than most contemporary surveys, the data is substantially more informative and can better clarify the results of efforts in seabird conservation and management.