Presencia religiosa

One of the earliest and most significant microcosm experiments in science dates back to 1772, whereby Joseph Priestley placed mice and mint plants in sealed jars, discovering the balance between ‘putrefying’ and ‘regenerative’ processes; the mice were able to respire using the oxygen produced by the plant and the plant was able to utilise the CO2 produced by the mouse (Gorham,

the earliest ecological experiments dates back to 1887 (Jessup et al., 2005). These were followed by some of the first examples and investigations of density dependence and succession in ecology (Woodruff, 1911, 1912, 1913, Herrando-Perez et al., 2012). Arguably the most influential ecological microcosm experiments were carried out by Gause (1934), who investigated interactions between bacteria, yeasts and protozoa, proving that two competitors cannot coexist on a single limiting resource, which to this day are a text book example of competition and predator-prey interactions (Begon et al.,2006). These important studies highlight that large scale processes can be elucidated from small scale investigations (Naeem, 2009). There are many advantages for using microbial microcosms to study ecological questions. For example, extremely high levels of experimental control and replication can be easily achieved. The short generation times of microorganisms allows

experiments running a matter of days or weeks to cover tens to thousands of generations and the ‘history’ of these experiments can be biologically archived by freezing samples at -80° (Bohannan & Lenski, 2000).

A large scale microcosm experiment was carried out by Whittebolle et al. (2009) which included over 1,260 microcosms. They used denitrifying bacterial communities to model the effects of

reduced biodiversity on the functional capabilities of the communities. Or more generally, they asked the question ‘how does reduced biodiversity effect ecosystem function?’ This study was one of the most elaborate of its kind and what made it unique was the focus solely on community evenness (a measure of the equality or distribution of individuals among species); most previous studies focused exclusively on the effect of reduced taxa richness on ecosystem function (Worm et al., 2006). The direct manipulation of community evenness is extremely difficult to achieve in natural ecosystems (Naeem, 2009). However, with the use of over 1,000 microcosms and modern laboratory equipment, Wittebolle et al (2009) were able to investigate the effects of reduced community evenness on ecosystem function. The experiment also coupled environmental stressors (temperature and salinity stress) with varying levels of community evenness. This was a major part of the experiment and it allowed an interesting and environmentally significant conclusion to be drawn. Decline in community evenness affects ecosystem function in a similar manner to taxa richness; reduced evenness leads to reduced ecosystem function. However, the magnitude of this effect seemed to depend on the level of environmental stress, with high stress and low evenness having the biggest detrimental effect on ecosystem function. This study, which was carried out on 96-well plates, where each ‘microcosm’ was actually an individual well, produced a Nature manuscript that catalysed wide debate across the whole field of ecology and environmental sciences.

The microcosm study of Bell (2010) (introduced in the ‘Distance-decay’ section) is a beautifully simple and eloquent experiment that produced interesting and insightful results. In this experiment, Bell placed microcosms (small glass jars in this instance) containing a sterile broth. A total of 112

microcosms were placed 71 m apart (that is, at: 0, 71, 142, 213, 284, 355, 426, 497 m) across a wooded study area (14 microcosms per site). The microcosms were then left to be colonised by atmospheric bacteria for 28 days although half of the microcosms at each site were closed to further colonisation after 14 days to prevent additional colonisation. Using a molecular fingerprinting technique ‘terminal restriction fragment length polymorphism’(tRFLP) Bell observed a significant positive relationship between physical distance and community dissimilarity for both sets of microcosms open for 14 and 28 days ). The advantage of this experiment was that is allowed the investigation of distance decay in natural bacterial communities among identical environmental conditions, as the same water was used to inoculate all microcosms. This is near on impossible to study or reproduce in the natural world due to high levels of heterogeneity.

Langenheder & Szekely (2011) used microcosms to investigate the early colonization of pristine (sterilised) marine microcosms. In this experiment, microcosms were inoculated with sterilised sea water sampled from three chemically distinct rock pools. These were then left open for 8.5 hours to allow atmospheric bacterial colonisation to occur; rain water was also collected during the

experiment. After this period all of the microcosms were sealed off and incubated in the laboratory for a further 5 days. DNA extractions were then carried out and DNA sequencing was performed. Langenheder & Szekely (2011) showed that significant differences were found in community composition relating to rock pool water source; evidence for species sorting. However, taxa that were abundant in the rain water samples were also abundant in the microcosms; evidence of neutral processes. Although this experiment only focussed on the colonisation of sterilised environments and during one colonisation period (8.5 hours), it provided insight into the factors that regulate bacterial communities during the very early stages of bacterial colonisation. These experiments highlight the power of hypothesis driven microcosm experiments to answer questions in microbial ecology.

This thesis utilised microcosm, mesocosm and natural aquatic systems to test the hypotheses described in this introduction, with a specific focus on species sorting and neutral processes. From the literature it is clear that microcosms/mesocosms systems can be used as excellent tools in hypothesis-driven science. It is no exaggeration that natural soil bacterial communities are extremely complex and very difficult to study in their natural environment due to the uneven distribution of bacteria among the soil matrix (Lombard et al., 2011). This problem has been even more confounded by the very high level of heterogeneity which occurs in soils (Ranjard & Richaume, 2001) producing a wide range of microniches which can be found within a single gram (Ding et al., 2013). These

problems mean microcosms are excellent means to study the ecological processes which regulate bacterial communities established in soils, as they allow high levels of control and regulation of external environments. The relatively higher levels of homogeneity found within aquatic systems makes them an even more suitable environment to study the key processes that regulate bacterial

communities. Because our knowledge of bacterial community ecology is still limited, aquatic systems are an excellent place to start, and it is highly likely similar or analogous processes are functioning in both aquatic and soil based environments. Even though microcosm experiments have proved to be very successful in studying aquatic microbial ecology, there are relatively few experimental studies aimed at investigating bacterial community assembly using hypothesis-driven science (Lindström & Langenheder, 2012). Of course, microbial ecologists still have to confront the issues of ‘ecological relevance’ revolving around microcosm studies; but these issues have been debated by ecologists since the dawn of the science itself (Srivastava et al., 2004). As long we accept that microcosms may represent simplified environmental systems, armed with well structured, interesting hypotheses, microcosms can be an excellent tool in the microbial ecologists’ toolbox.