A Novel Algorithm for the Determination of Bacterial Cell Volumes That is Unbiased by Cell Morphology

The determination of cell volumes and biomass offers a means of comparing the standing stocks of auto- and heterotrophic microbes of vastly different sizes for applications including the assessment of the flux of organic carbon within aquatic ecosystems. Conclusions about the importance of particular genotypes within microbial communities (e.g., of filamentous bacteria) may strongly depend on whether their contribution to total abundance or to biomass is regarded. Fluorescence microscopy and image analysis are suitable tools for determining bacterial biomass that moreover hold the potential to replace labor-intensive manual measurements by fully automated approaches. However, the current approaches to calculate bacterial cell volumes from digital images are intrinsically biased by the models that are used to approximate the morphology of the cells. Therefore, we developed a generic contour based algorithm to reconstruct the volumes of prokaryotic cells from two-dimensional representations (i.e., microscopic images) irrespective of their shape. Geometric models of commonly encountered bacterial morphotypes were used to verify the algorithm and to compare its performance with previously described approaches. The algorithm is embedded in a freely available computer program that is able to process both raw (8-bit grayscale) and thresholded (binary) images in a fully automated manne

A Novel Algorithm for the Determination of Bacterial Cell Volumes That is Unbiased by Cell Morphology

The determination of cell volumes and biomass offers a means of comparing the standing stocks of auto- and heterotrophic microbes of vastly different sizes for applications including the assessment of the flux of organic carbon within aquatic ecosystems. Conclusions about the importance of particular genotypes within microbial communities (e.g., of filamentous bacteria) may strongly depend on whether their contribution to total abundance or to biomass is regarded. Fluorescence microscopy and image analysis are suitable tools for determining bacterial biomass that moreover hold the potential to replace labor-intensive manual measurements by fully automated approaches. However, the current approaches to calculate bacterial cell volumes from digital images are intrinsically biased by the models that are used to approximate the morphology of the cells. Therefore, we developed a generic contour based algorithm to reconstruct the volumes of prokaryotic cells from two-dimensional representations (i.e., microscopic images) irrespective of their shape. Geometric models of commonly encountered bacterial morphotypes were used to verify the algorithm and to compare its performance with previously described approaches. The algorithm is embedded in a freely available computer program that is able to process both raw (8-bit grayscale) and thresholded (binary) images in a fully automated manner

Multi-spot live-image autofocusing for high-throughput microscopy of fluorescently stained bacteria

Screening by automated high-throughput microscopy has become a valuable research tool. An essential component of such systems is the autonomous acquisition of focused images. Here we describe the implementation of a high-precision autofocus routine for imaging of fluorescently stained bacteria on a commercially available microscope. We integrate various concepts and strategies that together substantially enhance the performance of autonomous image acquisition. These are (i) nested focusing in brightfield and fluorescence illumination, (ii) autofocusing by continuous life-image acquisition during movement in z-direction rather than at distinct z-positions, (iii) assessment of the quality and topology of a field of view (FOV) by multi-spot focus measurements and (iv) acquisition of z-stacks and application of an extended depth of field algorithm to compensate for FOV unevenness. The freely provided program and documented source code allow ready adaptation of the here presented approach to various platforms and scientific questions

Mesolithic domestic pigs at Rosenhof – or wild boar? A critical re-appraisal of ancient DNA and geometric morphometrics

We challenge the claim by Krause-Kyora et al. (2013) that there were domestic pigs at Mesolithic sites in northern Germany. A small number of animals from Rosenhof and Poel have ancient DNA and geometric morphometric signatures elsewhere associated with domestic animals. At this time Neolithic farming settlements were present 150km to the south, but the Mesolithic specimens are, however, metrically wild boar, much larger than domestic pigs, and cannot be domestic individuals acquired from the farmers. A more likely explanation for these ‘domestic’ traits is that animals that escaped from farmers’ pig herds interbred with local wild boar. Their descendants were morphologically and behaviourally wild, and were shot by Mesolithic foragers in the course of normal hunts. Their presence at Mesolithic sites is not a precursor to agriculture

Sodium iron EDTA and ascorbic acid, but not polyphenol oxidase treatment, counteract the strong inhibitory effect of polyphenols from brown sorghum on the absorption of fortification iron in young women

In addition to phytate, polyphenols (PP) might contribute to low Fe bioavailability from sorghum-based foods. To investigate the inhibitory effects of sorghum PP on Fe absorption and the potential enhancing effects of ascorbic acid (AA), NaFeEDTA and the PP oxidase enzyme laccase, we carried out three Fe absorption studies in fifty young women consuming dephytinised Fe-fortified test meals based on white and brown sorghum varieties with different PP concentrations. Fe absorption was measured as the incorporation of stable Fe isotopes into erythrocytes. In study 1, Fe absorption from meals with 17mg PP (8·5%) was higher than that from meals with 73mg PP (3·2%) and 167mg PP (2·7%; P<0·001). Fe absorption from meals containing 73 and 167mg PP did not differ (P=0·9). In study 2, Fe absorption from NaFeEDTA-fortified meals (167mg PP) was higher than that from the same meals fortified with FeSO4 (4·6 v. 2·7%; P<0·001), but still it was lower than that from FeSO4-fortified meals with 17mg PP (10·7%; P<0·001). In study 3, laccase treatment decreased the levels of PP from 167 to 42mg, but it did not improve absorption compared with that from meals with 167mg PP (4·8 v. 4·6%; P=0·4), whereas adding AA increased absorption to 13·6% (P<0·001). These findings suggest that PP from brown sorghum contribute to low Fe bioavailability from sorghum foods and that AA and, to a lesser extent, NaFeEDTA, but not laccase, have the potential to overcome the inhibitory effect of PP and improve Fe absorption from sorghum food

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences

Modeling resilience and sustainability in ancient agricultural systems

The reasons why people adopt unsustainable agricultural practices, and the ultimate environmental implications of those practices, remain incompletely understood in the present world. Archaeology, however, offers unique datasets on coincident cultural and ecological change, and their social and environmental effects. This article applies concepts derived from ecological resilience thinking to assess the sustainability of agricultural practices as a result of long-term interactions between political, economic, and environmental systems. Using the urban center of Gordion, in central Turkey, as a case study, it is possible to identify mismatched social and ecological processes on temporal, spatial, and organizational scales, which help to resolve thresholds of resilience. Results of this analysis implicate temporal and spatial mismatches as a cause for local environmental degradation, and increasing extralocal economic pressures as an ultimate cause for the adoption of unsustainable land-use practices. This analysis suggests that a research approach that integrates environmental archaeology with a resilience perspective has considerable potential for explicating regional patterns of agricultural change and environmental degradation in the past

Reply to Ellis et al.: human niche construction and evolutionary theory

We are pleased Ellis et al. found value in our recent synthesis of the deep history of human impacts on global ecosystems and agree that our paper should influence the current debate on if and how an Anthropocene epoch is defined. We also agree that the ecological consequences of human niche construction have profound and growing effects on the evolutionary trajectories of humans and other species living within human-altered ecosystems. Niche construction theory (NCT) provides an explicit framework for linking evolutionary and ecological processes into a coherent theory of biological evolution. Of special appeal to us as archaeologists is that NCT bridges biological and cultural evolution by including human culture and social learning within the mechanisms of evolutionary change, allowing scientists to address issues at the interface of human and natural systems. Some of us have contributed significantly to human NCT, addressing some of the very issues raised by Ellis et al. Finally, we agree that human transformations of ecosystems are inherently social processes—clearly humans are intensely social organisms—and that such processes result from long-term melding of biological and cultural evolution

Nowcasting of thunderstorm severity with Machine Learning in the Alpine Region

Presentación realizada en la 3rd European Nowcasting Conference, celebrada en la sede central de AEMET en Madrid del 24 al 26 de abril de 2019

Reply to Westaway and Lyman: emus, dingoes, and archaeology’s role in conservation biology

In a curious comment on our PNAS Perspective, Westaway and Lyman offer two Australian zooarchaeological case studies—one involving eggshells and the other dingoes—that they argue undercut one of our main points: that archaeological data and deep time perspectives have much to offer conservation biology. Neither example provides a specific substantive critique of our perspective: there are no dingoes in our article, no eggshells, and we mention the long and rich record of human management and alteration of Australian environments only briefly. Nor do we suggest that all archaeological assemblages can effectively inform current conservation biology efforts. Such datasets obviously vary in their quality and potential applicability to modern situations. When considered more closely, both of Westaway and Lyman’s case studies underscore rather than undercut the importance of archaeological and paleoecological data in conservation biology initiatives