Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

The role of phytoplankton composition and microbial community metabolism in sea-air Delta pCO₂ variation in the Weddell Sea

The Weddell Sea is known to be a CO2 sink due to active biological and physical pumps. Here we study the relationships of phytoplankton biomass and composition and microbial community metabolism, estimated from simulated in situ incubations and from nutrient's difference between surface and subsurface waters, with ?pCO2 in the Weddell Sea, during four austral summers (2002–2005). The ?pCO2 was significantly negative throughout the Weddell Sea in 2002 (-17.2±28.1 µatm), 2003 (-64.1±31.3 µatm), 2004 (-54.9±61.8 µatm) and 2005 (-63.8±60 µatm), indicating that the Weddell Sea acted as an atmospheric CO2 sink during those summers. The ?pCO2 was significantly lower in the south than in the center or north of the Weddell Sea. This was consistent with the significantly higher Chlorophyll-a concentrations (Chl-a) observed in the south (2.3±1.9 µg l-1) than in the center (1.3±1.2 µg l-1) or north (1.4±1.7 µg l-1). In contrast, waters were mainly undersaturated in O2, due to the upwelling of oxygen poor Warm Deep Water (WDW). The negative relationship between the ?pCO2 and the %O2 saturation suggested that planktonic metabolic activities played a role in these gases dynamics, along with the upwelling of WDW. However, these relationships could not be observed from the results of the incubation experiments, probably because of different temporal scales between gas exchanges in incubation experiments and in situ CO2 and O2 dynamics. The dynamics of CO2 and O2 were solely related to the net community production (NCP) and to the gross primary production (GPP) when only stations with Chl-a > 1 µg l-1 were considered. A significant relationship was, however, found between ?pCO2 and the primary production until the time of sampling for all stations when estimated from nutrients depletion between surface and subsurface waters. Finally, the distribution of CO2 and O2 were related to the biomass of diatoms and, contrarily to other seas, to the biomass of phytoflagellates

Effects of enhanced temperature and ultraviolet B radiation on a natural plankton community of the Beagle Channel (Southern Argentina): A mesocosm study

Marine planktonic communities can be affected by increased temperatures associated with global climate change, as well as by increased ultraviolet B radiation (UVBR, 280-320 nm) through stratospheric ozone layer thinning. We studied individual and combined effects of increased temperature and UVBR on the plankton community of the Beagle Channel, southern Patagonia, Argentina. Eight 2 m3 mesocosms were exposed to 4 treatments (with 2 replicates) during 10 d: (1) control (natural temperature and UVBR), (2) increased UVBR (simulating a 60% decrease in stratospheric ozone layer thickness), (3) increased temperature (+ 3°C), and (4) simultaneous increased temperature and UVBR (60% decrease in stratospheric ozone; + 3°C). Two distinct situations were observed with regard to phytoplankton biomass: bloom (Days 1-4) and post-bloom (Days 5-9). Significant decreases in micro-sized diatoms (>20 µm), bacteria, chlorophyll a, and particulate organic carbon concentrations were observed during the post-bloom in the enhanced temperature treatments relative to natural temperature, accompanied by significant increases in nanophytoplankton (10-20 µm, mainly prymnesiophytes). The decrease in micro-sized diatoms in the high temperature treatment may have been caused by a physiological effect of warming, although we do not have activity measurements to support this hypothesis. Prymnesiophytes benefited from micro-sized diatom reduction in their competition for resources. The bacterial decrease under warming may have been due to a change in the dissolved organic matter release caused by the observed change in phytoplankton composition. Overall, the rise in temperature affected the structure and total biomass of the communities, while no major effect of UVBR was observed on the plankton community

On the phytoplankton bloom in coastal waters of southern King George Island (Antarctica) in January 2010: An exceptional feature?

Since the early 1990s, phytoplankton has been studied and monitored in Potter Cove (PC) and Admiralty Bay (AB), King George/25 de Mayo Island (KGI), South Shetlands. Phytoplankton biomass is typically low compared to other Antarctic shelf environments, with average spring–summer values below 1 mg chlorophyll a (Chl a) m23. The physical conditions in the area (reduced irradiance induced by particles originated from the land, intense winds) limit the coastal productivity at KGI, as a result of shallow Sverdrup’s critical depths (Zc) and large turbulent mixing depths (Zt). In January 2010 a large phytoplankton bloom with a maximum of around 20 mg Chl a m23, and monthly averages of 4 (PC) and 6 (AB) mg Chl a m23, was observed in the area, making it by far the largest recorded bloom over the last 20 yr. Dominant phytoplankton species were the typical bloom-forming diatoms that are usually found in the western Antarctic Peninsula area. Anomalously cold air temperature and dominant winds from the eastern sector seem to explain adequate light : mixing environment. Local physical conditions were analyzed by means of the relationship between Zc and Zt, and conditions were found adequate for allowing phytoplankton development. However, a multiyear analysis indicates that these conditions may be necessary but not sufficient to guarantee phytoplankton accumulation. The relation between maximum Chl a values and air temperature suggests that bottom-up control would render such large blooms even less frequent in KGI under the warmer climate expected in the area during the second half of the present century

Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation Análise molecular da diversidade bacteriana de um consórcio degradador de óleo diesel

Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by PCR reaction using specific oligonucleotide primers for the 16S rRNA gene. The PCR products were cloned into a pGEM-T-Easy vector (Promega), and Escherichia coli was used as the host cell for recombinant DNAs. The partial clone sequencing was obtained using universal oligonucleotide primers from the vector. The genetic library obtained generated 431 clones. All the sequenced clones presented similarity to phylum Proteobacteria, with Gammaproteobacteria the most present group (49.8 % of the clones), followed by Alphaproteobacteira (44.8 %) and Betaproteobacteria (5.4 %). The Pseudomonas genus was the most abundant in the metagenomic library, followed by the Parvibaculum and the Sphingobium genus, respectively. After partial sequencing of the 16S rRNA, the diversity of the bacterial consortium was estimated using DOTUR software. When comparing these sequences to the database from the National Center for Biotechnology Information (NCBI), a strong correlation was found between the data generated by the software used and the data deposited in NCBI.<br>O óleo diesel é um composto derivado do petróleo, constituído basicamente por hidrocarbonetos. Condições precárias no processo de transporte e armazenagem desse produto contribuem significativamente para derrames acidentais, ocasionando sérios problemas ecológicos no solo e água, alterando assim toda a diversidade microbiológica do ambiente. A estratégia de clonagem e sequenciamento do gene 16S rRNA é uma das técnicas moleculares que permitem estimar e comparar a diversidade microbiana de diferentes amostras ambientais, sejam elas impactadas ou não. O objetivo deste trabalho foi estimar a diversidade de microrganismos pertencentes ao domínio Bacteria em um consórcio degradador de óleo diesel por meio de sequenciamento parcial do gene 16S rRNA. Após extração do DNA metagenômico, o material foi amplificado por reação de PCR com oligonucleotídeos iniciadores específicos para o gene 16S rRNA. Os produtos da reação de PCR foram clonados em vetor pGEM T Easy (Promega) e transformados em células competentes de Escherichia coli. O sequenciamento parcial dos clones foi feito com oligonucleotídeos universais do vetor. A biblioteca obtida gerou 431 clones. Todos os clones mostraram similaridade com o filo Proteobacteria, onde as Gammaproteobacteria compreenderam o grupo de maior representatividade, com 49,8 % dos clones, seguida das Alphaproteobacteira, com 44,8 %, e das Betaproteobacteria, com 5,4 %. O gênero Pseudomonas destacou-se como representante com maior frequência de clones na biblioteca, seguido pelos gêneros Parvibaculum e Sphingobium. Após o sequenciamento parcial do gene 16S rRNA, a diversidade bacteriana do consórcio foi estimada utilizando-se o software DOTUR. Essas sequências, quando comparadas com as do banco do National Center for Biotechnology Information (NCBI), mostraram grande correlação entre os dados gerados pelo software utilizado e aqueles depositados no NCBI

Reporting guidelines for human microbiome research: the STORMS checklist

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results