please do the both questions Q1: Explain what table 1 shows, and how do the resu
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please do the both questions
Q1: Explain what table 1 shows, and how do the results support or refute the paper’s main points.
Q2: Explain what table 2 shows, and how do the results support or refute the paper’s main points.
The majority of microorganisms from natural environments cannot be grown in the laboratory. The diffu- sion-chamber-based approach is an alternative method that allows microorganisms to grow in their natural environment. An inoculum is sandwiched between semipermeable (0.03-?m-pore-size) membranes of the chamber, which is then returned to the source environment. The chamber allows for a free exchange of chemicals with the external milieu by diffusion while restricting the movement of cells. We used freshwater pond sediment to inoculate diffusion chambers and petri dishes. The difusion chambers were incubated on top of the sediment for 4 weeks. Both chamber and petri dish cultivation resulted in the isolation of numerous representatives of Alpha-, Beta-, and ever, the diffusion-chamber-based approach also led to the isolation of species from rarely cultivated groups, such as Deltaproteobacteria, Verrucomicrobia, Spirochaetes, and Acidobacteria. Material from the chambers was also transferred to new chambers in order to learn whether this will increase the recovery isolates could be obtained only from material transferred through multiple diffusion chambers. This suggests that continuous cultivation in diffusion chambers adapts some microorganisms for growth under otherwise prohibitive in vitro conditions. ; Actinobacteria; Firmicutes; and Bacteroidetes. How of isolates. Several The majority of microorganisms from environmental sam ples cannot be cultivated with the widely used laboratory meth velopment of new isolation methods. ods (16, 22, 28). Large discrepancies between the number of We developed a diffusion chamber approach (Fig. 1) that CFU and direct cell counts were observed as early as the provided access to up to 40% of the cells present in a marine beginning of the last century (1, 10) and repeatedly confirmed sediment environment (21). The approach is based on placing in numerous publications (3, 8, 18, 36). Culture-independent microorganisms in a diffusion chamber separated from the molecular methods showed that uncultivated species represent environment by 0.03-?m-pore-size membranes and incubating the bulk of the microbial diversity on our planet (16, 28), with the chamber in the natural habitat of the target microorgan more than half of the discovered bacterial phyla having no or isms. The membranes are permeable by molecules of various only a few cultured members (9, 22, 28). Gaining access to sizes as well as small viruses. Diffusion provides the cells witlh these microorganisms is of substantial basic and applied sig- access to their naturally occurring growth components, includ nificance. Several cultivation approaches have been suggested ing nutrients and possible signaling compounds, and removes and developed to address the "great plate count anomaly"the metabolic products. Preliminary observations (T. Kaeber- (31). A high-throughput approach based on dilution to extinc ein and D. Nichols, unpublished) showed that some environ- tion with seawater as the substrate led to cultivation of repre mental microorganisms might acquire the ability to grow ina sentatives of the very abundant but previously uncultivated petri dish after repeated cultivation in a diffusion chamber. We alphaproteobacterial clade SAR11 (11, 26). Another high- confirm these observations by showing that one to several throughput approach successfully used single-cell encapsula- incubations in a diffusion chamber lead to an increase in the tion and cocultivation of environmental microorganisms to number and diversity of environmental isolates capable of increase microbial recovery (35). The addition of cyclic AMPgrowth in vitro. and homoserine lactones to the growth media also produced additional microbial isolates (5, 6, 7, 32). The manipulation of growth medium composition and increased length of incuba tion led to the isolation of Acidobacteria and Vemucomicrobia (12, 19, 20, 29, 32). However, the majority of environmental remain uncultivated, and this calls for the de MATERIALS AND METHODS Sampling. Sediment and water samples were taken in the fall of 2004 from Turtle Pond, a small freshwater pond in Boston, MA. A freshly collected block of near-shore sediment was carefully placed in a 30- by 40-cm aquarium to forrm a 10-cm-thick layer. The sediment was kept in the lab under 5 cm of pond water with continuous acration. Over the course of the growth experiment (16 wecks; see below), the sediment was replaced twice with freshly collected material. Corresponding author. Mailing address: Northeastern University Department of Biology, 134 Mugar Life Science Building, 360 Hun- tington Ave Boston, MA 02115. Phone: 617 373-4048 Fax: 617 373-3724. E-mail: s.epstein@neu.edu. Media. The media (all from Difco, Becton, Dickinson & Company, Sparks, MD) used in the isolation experiments were prepared with 1.5% Bacto agar and 10% sterile filtered pond water. The following media were supplemented with the indicated carbon sources: medium A, no supplements; C, 0.01% Bacto Casamino Acids; E 0.1% hot water extract from the source sediment (see below); CY, 0.01% Bacto Casamino Acids and 0.01% Bacto yeast extract; CYE, 0.01% Bacto Casamino Acids, 0.01% Bacto yeast extract, and 0.1% hot water extract from the source sediment; and Y, 0.01% Bacto yeast extract. Hot water extract was prepared by mixing sediment and deionized water in a 1:10 ratio. The ?Present address: Miami University, Department of Microbiology, 32 Pearson Hall, Oxford, OH 45056. t Supplemental material for this article may be found at http://aem asm.org Published ahead of print on 24 August 2007 6386Explanation / Answer
The main focus of the paper is whether it is possible to microorganisms in the laborytory setup instead of their natural environment. They have used two different method- a petridish culture and a diffusion based chamber to isolate and grow microorganisms. They have collected the microorganisms from fresh water pond and then tried to isolate and grow them for generation with these methods. Both of these methods were successful to isolet different microorganisms inviro which are present in the fresh water environments . Additionally they have also found that when they are using diffusion based approach microorganisms can also grown for several generaion which otherwise seems not possible in a invitro situation.
Now, if we look at the table-1, this one describes few things-
i) which microorganisms have been isolated
ii) the no of each microorganisms isolated by petridish and diffusion chamber method. Additionally for the diffusion chamber they have also showed how many generation each microorganisms were grown and what was there number in each generation.
iii) Also total no of microorganisms which have been isolated by these two methods
this is the first thing we want to know from the study.
Table 2
Now among the microorganisms which they have isolated, few were already isolated by other groups. So at these point they required to confirm that the microorganisms which they have isolated by their method of choice is same with what was confirmed previously. To confirm this they use 16sRNA sequence. 16sRNA is a part of the 30S ribosome subunit of prokaryotes. 16sRNAs are often studied to evaluate the relationship between organisms as this region has been found to evolve slowly. So if microorganisms are showing similarity on their 16sRNA sequence we can say that they are represnting the same microorganisms.
IN table 2 that was the reason the authors check for 16sRNA sequence for the microorganisms they have isolated by these two methods and checked for sequence similarity with previously reported one. In table 2 , they reported the percentage of similarity of the 16sRNA between the previously cultured relative and with the newly isolated one. Then how many of them were isolated on petridish and with diffusion chamber method, and also with the microorganisms over the generation.
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