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...sity in the sediment. Previous studies demonstrated that pH, temperature and certain inorganic and organic contaminants are the most important drivers of the bacterial communities in sediment or soil =-=[57,60,61]-=-. Among pH, certain compounds (TOC, NH3-N, NO2 2-N, and NO3 2-N) and temperature in our study, TOC was found to be the primary driver that affected variability of bacterial density (qPCR for 16 S rRNA...

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...eria (8.1%), 5) Firmicutes (5.7%) and 6) Actinobacteria (4.5%) with the remaining bacterial phylum combining to 20% (Figure 2) and these taxa have been previously found to be highly abundant in soils =-=[61,62]-=-. When we tested for individual taxon responses at 93% SIL we found that treatment interactions accounted for the majority of the significant effects, suggesting that the responses of bacterial taxa a...

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...as having controlson soil fungal communities (Mouhamadou et al., 2013).sSome examples show that bacterial community composition and diversity stronglysrespond to soil pH, land use, and plant species (=-=Nacke et al., 2011-=-). It is also influencedsby restoration status (agriculturally affected vs. restored wetlands) whereas it does notsrespond as strongly to nutrient concentrations and not at all to wetland type or soil...

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...sity in the sediment. Previous studies demonstrated that pH, temperature and certain inorganic and organic contaminants are the most important drivers of the bacterial communities in sediment or soil =-=[57,60,61]-=-. Among pH, certain compounds (TOC, NH3-N, NO2 2-N, and NO3 2-N) and temperature in our study, TOC was found to be the primary driver that affected variability of bacterial density (qPCR for 16 S rRNA...

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...ired, even though part of the information could inevitably be lost [14]. Figure 1. Schematic drawing of the different approaches applied to study the rhizosphere microbial community and its interaction with host plants. The picture reports also the expected outcome from the application of the different analytical techniques. To date, the majority of the studies aiming at studying the composition of the soil microbial communities have been based on 16S rRNA profiling giving a taxonomical snapshot of the populations, in terms of relative abundance and diversity of bacteria and archea (Figure 1) [9,15, 16, 17, 18, 19, 20]. To further implement the taxonomical description of a microbial population, bioinformatic tools, as for instance the algorithm PICRUSt, can be exploited to predict the community’s putative functional capabilities on the base of 16SrRNA gene [21]. Nonetheless, the information provided is still indirect evidence and this approach may fail in completely describing the functional diversity and the characterizing aspects of the plant-associated microbiome [22]. However, this approach does not consider the horizontal gene transfer where genes integrated in different mobile genetic elements (plasmi...

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.... Though not described explicitly as an oligotroph [44], α-Proteobacteria have, in fact, been found to respond in a similar manner as Acidobacteria to oligotrophic environments in a number of studies =-=[11,45,46]-=-, as well as the current study. Concerning Bacteroidetes, the phyla did not seem to be negatively impacted in the TSS, although it has been associated with soil sediments. What may be more significant...

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...ermed ‘Hydric’. Later investigators focussed on the pH link (Fierer and Jackson, 2006; Lauber et al., 2009) but other factors such as organic matter quality have also more recently been investigated (=-=Nacke et al., 2011-=-; Davinic et al., 2012) and grouped into Fertility. We selected the term Fertility to explicitly link this latent variable to the notion of what is available for heterotrophic activity and what nutrie...

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...인되 었고, 여기에 속하는 Alteromonadales목, Oceanospirillales목, Rhizobiales목, Rhodobacterales목의 근권세균이 확인되었다 (Table 3). 기존 연구결과를 보았을 때, 토양에 존재하는 세균s중 방선균문과 프로테오박테리아문, 그리고 아키도박테리움 균(Acidobacteria)문이 우점하는 것을 알 수 있다=-=[13, 14, 18, 20, 21]-=-.　아키도박테리움균문은 난배양성 토양세균으로, 토양 에는 많이 존재하나 배양상의 어려움을 가지고 있다. 따라서s본 실험의 결과 자생식물의 근권에서 분리된 세균이 방선균문 과 프로테오박테리아문에 우점하는 것은 기존의 데이터와 많 은 부분 일치함을 알 수 있었다. 독도에 자생하는 해양 식물로부터 분리된 근권세균의 유전 학적 다양성을 확인하기 위하여 Shanno...

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...wever,scomparison of observed and predicted richness between studies is challenging as the outcome issgreatly influence by sequencing depth and the hypervariable region of the 16S rRNA beingsanalyzed =-=[38]-=-. Therefore, comparison of diversity indices that compensate for sampling depth offer asmore robust method of comparing between studies. The Shannon Diversity Index calculated for thesBay of Fundy sed...