3 research outputs found
Molecular ecology of key organisms in sulfur and carbon cycling in marine sediments
The World s oceans host a variety of sulfidic habitats. Yet, microorganisms oxidizing reduced inorganic sulfur compounds have mostly been studied at hydrothermal vents, in anoxic basins, conspicuous microbial mats and symbioses but rarely in coastal sediments. In this thesis sulfur-oxidizing prokaryotes (SOP) of a eutrophic intertidal sand flat in the German Wadden Sea were investigated by molecular techniques. The diversity, abundance and activity of SOP were analyzed in particular among the Gammaproteobacteria. Comparative sequence analysis of the 16S rRNA and three genes involved in sulfur oxidation revealed a high diversity of mainly gammaproteobacterial SOP. Most of them were closely related to thiotrophic symbionts, including those of the tubeworm genus Oligobrachia. A group of free-living relatives accounted for up to 4% of all cells (~1.3 Ă— 108 cells ml-1). Consistent with a presumed chemolithoautotrophic utilization of inorganic sulfur compounds, these and numerous other members of the Gammaproteobacteria incorporated 14CO2 as revealed by microautoradiography (MAR). The findings demonstrate that non-filamentous Gammaproteobacteria are important catalysts of sedimentary sulfur oxidation and contribute to CO2-fixation in coastal surface sediments. Similarly, Roseobacter clade bacteria (RCB) accounted for unexpectedly high abundances of up to 10% of all cells in surface sediments (~2.5 Ă— 108 cells ml-1). A RCB-related genome fragment of 35 kb was recovered from a metagenomic fosmid library. It encoded genes of the SOX multienzyme system including the sulfur dehydogenase SoxCD, but also the complete rDSR pathway, a gene arrangement that is unique among SOP. Gene-targeted FISH confirmed the presence of the gene dsrA in sedimentary RCB enriched in anaerobic sulfidic medium. In addition, a novel gene, which encodes a putative dioxygenase, designated as dsrU, was identified in the rDSR pathway. Protocols were developed for application of MAR and nano-scale secondary ion mass spectroscopy (nanoSIMS) to marine sediment samples to follow assimilation of acetate in single cells. Members of the Gammaproteobacteria appeared to assimilate slightly more acetate than RCB, whereas sulfate-reducing bacteria showed no significant incorporation. Particularly the combination of flow cytometry and nanoSIMS proved to be powerful for up-scaling of the analysis of substrate uptake by sediment bacteria enabling an efficient, high-resolution profiling of single cells from complex microbial communities
The herpetofauna of the Eastern Afromontane: evolutionary history, biogeography and conservation
There is consensus that we are in the midst of the sixth great mass extinction
(Barnosky et al., 2011), with a current rate of extinction around 1,000 times the
background rate. Current extinction risk has, however, been formally evaluated for
less than 5% of the world's described species, but information on the proportion of
total species assessed and threatened offers a clear indication of the current trend of
biodiversity loss (Baillie et al., 2004). The situation is particularly critical for the class
Amphibia, with nearly one-third (32%) of the world’s amphibian species listed as
threatened (IUCN, 2014). The Eastern Afromontane region is one of the most diverse
areas on the Earth. A large proportion of its biodiversity and underlying evolutionary
history is concentrated in small forest fragments on mountains, where both ancient
lineages and more recently speciated taxa co-occur and a large proportion of the
currently known taxa is formally undescribed. Compared to other tropical areas of the
planet, East Africa has been characterized by pronounced climatic and geological
turbulence, which, has led to a general faunal impoverishment. Despite this, the
combination of the age of the forest fragments, their geographic and ecological
isolation and the habitat persistence, makes the vast complex of forest fragments an
ancient and stable archipelago of individually evolving sites, especially for the less
vagile organisms. Research that assesses the actual patterns of diversity of the region
and the definition of the most appropriate conservation strategies that can be effective
in a world changing at unprecedented rate is crucial and timely. The aims of this PhD
were to investigate historical and current biogeography of the herpetofauna of the
Eastern Afromontane, to describe patterns of species richness and endemism across
the region and to identify some of the main environmental drivers that have played a
significant role in shaping the current scenario. Focused analyses on forest vipers
(Atheris) and on dwarf forest bufonids (Nectophrynoides) were carried out in order to
understand elements of evolutionary history of the herpetofauna across the region and
to prioritize sites for conservation.
Chapter 2 focuses on the past and present of herpetological discoveries in the
Eastern Afromontane region and identified priority areas where future research could
lead to significant herpetofaunal discoveries. I discuss how survey effort, different
taxonomic approaches and the use of biodiversity indexes, have important implications for our understanding of the importance of individual sites since both
species delimitation methods and the use of indices capture different aspects of
biological diversity. The chapter includes 5 appendixes of which three are published
papers – two on the description of species new to science and one is a herpetological
inventory of a previously overlooked submontane forest in Tanzania. In the fourth
appendix I identify priority sites for further inventories (e.g Gura Ferda in Ethiopia,
Imatong Mts. in South Sudan, Itombwe and Misotshi-Kabogo ranges in DRC and Mt.
Chiperone in Mozambique). The fifth appendix introduces a work-in-progress to
publish an e-book on the region’s amphibians and reptiles, which will aid inventory
and ecological work across the region.
Chapter 3 investigates patterns of species richness and endemism of mountainrestricted
amphibians across the Eastern Afromontane region by mapping the
distributions of 3,488 geo-referenced records of 274 taxa. Results show a strong
geographical congruence between species richness and endemism and how the
Albertine Rift and the Eastern Arc mountains appear to have accumulated high
amphibian diversity in different ways, with the latter having exceptional diversity
despite their small sizes. Finally, results failed to support the idea that the Eastern
Afromontane is a discrete zoogeographic region.
Chapter 4 focuses on the phylogenetic relationships and historical
biogeography of the East African vipers in the genus Atheris and explores temporal
and spatial relationships between the different species across Africa. Results showed
congruent temporal patterns that link diversification to major tectonic and aridification
events within East Africa over the last 15 million years. This points to a
diversification pattern of the East African species consistent with a scenario of a
delayed direct West-East colonization of the Eastern Arc Mountains, influenced by the
formation of the western rift. Possible cryptic taxa in the Atheris genus are also
identified. Chapter 5 examined radiations and evolution of forest-associated toad in
the genus Nectophyrnoides, through phylogenetic reconstruction, finding that the
Eastern Arc Mountains are characterized by the presence of both very ancient paleoendemic
species, along with more recent radiations. I then identify key conservation
sites using different importance metrics. Congruence between richness of
Nectophrynoides and amphibians as a whole was strongly positive, suggesting that
this now better-known and conspicuous group could act as a proxy for assessing
relative importance of sites for amphibians generally. The high spatial and elevational turnover of Nectophrynoides species indicates the importance of conserving forest at
all altitudes and across the entire fragments in order to address the differences that
exist between sites at different altitudes, within the same fragment, and at similar
altitudes in different fragments on the same mountain block.
The results of this thesis highlight the biological importance of the Eastern
Afromontane as a key area for the study of the evolution of life and biodiversity
conservation, both at African and global levels. It provides original, updated
knowledge on species occurrence and biogeographic pattern at regional level. Results
also provide and interpretation of the signature left by geographic and climatic events
in the pattern of species diversification, clarifying the importance of specific historical
events in shaping what we see across the Eastern Afromontane today.
The recent surge in biodiversity studies, including the remarkable increase in
species description, represents a significant advance in geographic sampling and this,
coupled with the effectiveness of new methods for delimiting species, is helping in the
assessment of the actual biological value of areas. Furthermore the increasing
availability of genetic information on taxa should promote the use of phylogenetic
indexes in order to move from a conservation approach solely based on species
richness to a more inclusive one, that can inform conservation on the underlying
functional diversity and evolutionary potential both at species and site level.
The Eastern Afromontane represents the most important area of mainland
Africa for conservation of amphibians and reptiles and it offers an extraordinary
conservation challenge. Because of the extreme species turnover across mountain
ranges and individual forest fragments, a small number of protected areas, however
well managed and resourced, will never fully capture the biodiversity of the region.
Thus, a specific strategy aimed at identification and implementation of conservation
initiatives at forest fragment scale must be considered. Moreover, as a reaction to a
lucid assessment of global trends in population growth and associated habitat and
species loss and increasing resource demands, there is an urgent need to try new
conservation approaches. In the context of a more holistic and radical approach to
biodiversity conservation, an active management of the surrounding matrix of the
protected areas should be taken into consideration, with the aim of maintaining
connectivity between areas of less disturbed habitat and to minimize damage to
biodiversity, for unprotected lands, where resource extraction, agriculture, and other
productive activities occur