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Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage

Aida AA, Hatamoto M, Yamamoto M, Ono S, Nakamura A, Takahashi M, et al.

J Biosci Bioeng, 2014 Nov;118(5):540-5.
PMID: 24930844 DOI: 10.1016/j.jbiosc.2014.04.011

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors.
Estrous cycle based on blood progesterone profiles and changes in vulvar appearance of Malayan tapirs (Tapirus indicus)

Kusuda S, Ikoma M, Morikaku K, Koizumi J, Kawaguchi Y, Kobayashi K, et al.

J. Reprod. Dev., 2007 Dec;53(6):1283-9.
PMID: 17965541

The progesterone (P(4)) profiles and macroscopic vulvar changes of female Malayan tapirs were investigated in order to understand their fundamental reproductive physiology and to search for visual indicators of estrus. Blood was collected once or twice a week from seven female Malayan tapirs kept at four zoos. Serum or plasma P(4) concentrations were determined by radioimmunoassay. The P(4) concentrations changed cyclically throughout the years, and a total of 56 cycles was confirmed in the seven females. The length of the estrous cycle based on the P(4) profiles was 43.6+/-2.0 days; however, this mean includes great variation in length, from 21 to 84 days. Mucous discharge from the vulva and vulvar swelling were seen when the P(4) concentrations were low before the beginning of a rise in most cases. In conclusion, captive female Malayan tapirs have variations of approximately 1 to 3 months in estrous cycle length, and visual changes in the vulva are helpful in estimating estrus in female Malayan tapirs.
Fulltext Forests and Their Canopies: Achievements and Horizons in Canopy Science

Nakamura A, Kitching RL, Cao M, Creedy TJ, Fayle TM, Freiberg M, et al.

Trends Ecol Evol, 2017 06;32(6):438-451.
PMID: 28359572 DOI: 10.1016/j.tree.2017.02.020

Forest canopies are dynamic interfaces between organisms and atmosphere, providing buffered microclimates and complex microhabitats. Canopies form vertically stratified ecosystems interconnected with other strata. Some forest biodiversity patterns and food webs have been documented and measurements of ecophysiology and biogeochemical cycling have allowed analyses of large-scale transfer of CO2, water, and trace gases between forests and the atmosphere. However, many knowledge gaps remain. With global research networks and databases, and new technologies and infrastructure, we envisage rapid advances in our understanding of the mechanisms that drive the spatial and temporal dynamics of forests and their canopies. Such understanding is vital for the successful management and conservation of global forests and the ecosystem services they provide to the world.
Fulltext Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

Ji Y, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A, et al.

Ecol Lett, 2013 Oct;16(10):1245-57.
PMID: 23910579 DOI: 10.1111/ele.12162

To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.
Fulltext Spatial scale changes the relationship between beta diversity, species richness and latitude

Sreekar R, Katabuchi M, Nakamura A, Corlett RT, Slik JWF, Fletcher C, et al.

R Soc Open Sci, 2018 Sep;5(9):181168.
PMID: 30839691 DOI: 10.1098/rsos.181168

The relationship between β-diversity and latitude still remains to be a core question in ecology because of the lack of consensus between studies. One hypothesis for the lack of consensus between studies is that spatial scale changes the relationship between latitude and β-diversity. Here, we test this hypothesis using tree data from 15 large-scale forest plots (greater than or equal to 15 ha, diameter at breast height ≥ 1 cm) across a latitudinal gradient (3-30o) in the Asia-Pacific region. We found that the observed β-diversity decreased with increasing latitude when sampling local tree communities at small spatial scale (grain size ≤0.1 ha), but the observed β-diversity did not change with latitude when sampling at large spatial scales (greater than or equal to 0.25 ha). Differences in latitudinal β-diversity gradients across spatial scales were caused by pooled species richness (γ-diversity), which influenced observed β-diversity values at small spatial scales, but not at large spatial scales. Therefore, spatial scale changes the relationship between β-diversity, γ-diversity and latitude, and improving sample representativeness avoids the γ-dependence of β-diversity.
Fulltext Reproductive factors and risk of mortality in the European Prospective Investigation into Cancer and Nutrition; a cohort study

Merritt MA, Riboli E, Murphy N, Kadi M, Tjønneland A, Olsen A, et al.

BMC Med, 2015 Oct 30;13:252.
PMID: 26515238 DOI: 10.1186/s12916-015-0484-3

BACKGROUND: Reproductive events are associated with important physiologic changes, yet little is known about how reproductive factors influence long-term health in women. Our objective was to assess the relation of reproductive characteristics with all-cause and cause-specific mortality risk.
METHODS: The analysis was performed within the European Investigation into Cancer and Nutrition prospective cohort study, which enrolled >500,000 women and men from 1992 to 2000, who were residing in a given town/geographic area in 10 European countries. The current analysis included 322,972 eligible women aged 25-70 years with 99 % complete follow-up for vital status. We assessed reproductive characteristics reported at the study baseline including parity, age at the first birth, breastfeeding, infertility, oral contraceptive use, age at menarche and menopause, total ovulatory years, and history of oophorectomy/hysterectomy. Hazard ratios (HRs) and 95 % confidence intervals (CIs) for mortality were determined using Cox proportional hazards regression models adjusted for menopausal status, body mass index, physical activity, education level, and smoking status/intensity and duration.
RESULTS: During a mean follow-up of 12.9 years, 14,383 deaths occurred. The HR (95 % CI) for risk of all-cause mortality was lower in parous versus nulliparous women (0.80; 0.76-0.84), in women who had ever versus never breastfed (0.92; 0.87-0.97), in ever versus never users of oral contraceptives (among non-smokers; 0.90; 0.86-0.95), and in women reporting a later age at menarche (≥15 years versus <12; 0.90; 0.85-0.96; P for trend = 0.038).
CONCLUSIONS: Childbirth, breastfeeding, oral contraceptive use, and a later age at menarche were associated with better health outcomes. These findings may contribute to the development of improved strategies to promote better long-term health in women.
Fulltext The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, et al.

Ecol Evol, 2014 Dec;4(24):4701-35.
PMID: 25558364 DOI: 10.1002/ece3.1303

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
Fulltext The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, et al.

Ecol Evol, 2017 Jan;7(1):145-188.
PMID: 28070282 DOI: 10.1002/ece3.2579

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.