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Diversity, Volume 2, Issue 7 (July 2010), Pages 959-1047

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Research

Jump to: Review

Open AccessArticle Identity Reconfiguration of Immigrants in Portugal
Diversity 2010, 2(7), 959-972; doi:10.3390/d2070959
Received: 31 May 2010 / Accepted: 23 June 2010 / Published: 1 July 2010
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Abstract
The starting point is the principle that there is no immigrant culture, but rather, different ways of living, coexisting and identifying oneself within the cultural worlds that each subject crosses on his or her social path. Here we study Brazilian immigrants in [...] Read more.
The starting point is the principle that there is no immigrant culture, but rather, different ways of living, coexisting and identifying oneself within the cultural worlds that each subject crosses on his or her social path. Here we study Brazilian immigrants in Portugal, working with the first wave (starting at the end of the 1980s) and the second wave (at the turn of the 20th to 21st century). We intend, firstly, to show how identity is reconstructed between two banks: the departure culture and the arrival culture. Secondly, we intend to give a voice to the most silent in the understanding of immigrants: the process of identity reconstruction of Brazilian immigrants is presented, resulting from ethno-biographic interviews. We will consider the cultural transfusion theory and observe the heterogeneous ways of living between cultures, whether by rejecting the departure culture (the Oblato‘s case), refusing the arrival one at a given moment (the mono-cultural subject according to the source culture), living in an ambivalent manner between the two (the multicultural self), or, finally, inventing a third bank, as the poets say, which corresponds to an attitude of including the cultural differences through which one crosses during his or her life history in an intercultural self (the Intercultural Transfuga). Full article
(This article belongs to the Special Issue Ethnic Diversity and Cultural Pluralism)
Open AccessArticle TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels
Diversity 2010, 2(7), 1015-1025; doi:10.3390/d2071015
Received: 16 June 2010 / Revised: 14 July 2010 / Accepted: 19 July 2010 / Published: 21 July 2010
Cited by 27 | PDF Full-text (387 KB) | HTML Full-text | XML Full-text
Abstract
The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes [...] Read more.
The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org. Full article
(This article belongs to the Special Issue Microbial Diversity: From the Biosphere to the Human Microbiome)
Open AccessArticle Molecular Characterization of the Archaeal Community in an Amazonian Wetland Soil and Culture-Dependent Isolation of Methanogenic Archaea
Diversity 2010, 2(7), 1026-1047; doi:10.3390/d2071026
Received: 10 June 2010 / Revised: 14 July 2010 / Accepted: 15 July 2010 / Published: 22 July 2010
Cited by 9 | PDF Full-text (658 KB) | HTML Full-text | XML Full-text
Abstract
Tropical wetlands are the major natural source of methane released into the atmosphere, producing about 60% of all natural emissions. The great wetland areas of the Amazon basin are the largest source of methane in this region, contributing an estimated 5% of [...] Read more.
Tropical wetlands are the major natural source of methane released into the atmosphere, producing about 60% of all natural emissions. The great wetland areas of the Amazon basin are the largest source of methane in this region, contributing an estimated 5% of the total emissions from the world’s flooded areas. However, despite the important role that methanogenic archaea play in these environments, there have been few studies on the composition of their archaeal communities. In this survey, four 16S rRNA archaeal clone libraries from different depths were constructed to examine the archaeal community in an Amazon wetland soil. A total of 599 clones were used to perform diversity and phylogenetic analyses. A broad, diverse archaeal community was found at the site, with the diversity decreasing as the depth increased (Shannon index range: 2.40–1.94). Phylogenetic analysis revealed sequences belonging to two archaeal phyla, with 65% classified as Crenarchaeota and 35% classified as Euryarchaeota. Within the Euryarchaeota group, most sequences were clustered into the Methanococci and Methanomicrobia classes, two groups of methanogens. Based on the abundance of methanogenic organisms, culture–dependent isolation was used to isolate these organisms. To enhance the growth of methanogenic archaea, a modified atmosphere (H2:CO2 = 80:20) was established combined with an anoxic environment for 18 months. Among the isolates, the genera Methanosarcina and Methanobacterium were detected throughout the anaerobic in vitro cultivation, indicating a possible role for these organisms in methane production. In conclusion, these exploratory molecular and culture–dependent approaches enhance our understanding of the archaeal community and methanogenic archaea living in wetland soils of the eastern Amazon and their role in methane production. Full article
(This article belongs to the Special Issue Microbial Diversity: From the Biosphere to the Human Microbiome)

Review

Jump to: Research

Open AccessReview Methods to Estimate the Diversity in the Marine Photosynthetic Protist Community with Illustrations from Case Studies: A Review
Diversity 2010, 2(7), 973-1014; doi:10.3390/d2070973
Received: 23 June 2010 / Revised: 9 July 2010 / Accepted: 10 July 2010 / Published: 16 July 2010
Cited by 23 | PDF Full-text (774 KB) | HTML Full-text | XML Full-text
Abstract
We review the application of molecular methods to estimate biodiversity in the marine environment. All of the methods reviewed here, which are at the forefront of molecular research, can be applied to all organisms in all habitats, but the case studies used [...] Read more.
We review the application of molecular methods to estimate biodiversity in the marine environment. All of the methods reviewed here, which are at the forefront of molecular research, can be applied to all organisms in all habitats, but the case studies used to illustrate the points are derived from marine photosynthetic eukaryotic protists. It has been accepted that we know less than 10% of the identified diversity in the marine microbial world and the marine micro- and pico-eukaryotes are no exception. Even the species that we think we can easily recognize are often poorly described, and even less is known of their life histories and spatial and temporal trends in their abundance and distribution. With new molecular and analytical techniques, we can advance our knowledge of marine biodiversity at the species level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience. Biogeochemical reactions performed by marine photosynthetic microbial organisms constitute a major sustaining component of ecosystem functioning, and therefore, affect climate changes. New interpretations of how environmental, ecological and evolutionary processes control and structure marine ecosystem biodiversity can be made so that we can augment our understanding of biodiversity and ecosystem dynamics in especially the pico- and nano-fractions of the plankton as well as in the deep sea benthos, both of which are very difficult to study without good analytical methods. Full article
(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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