Expected Outline and first (self) thoughts:

Introduction: (4 Pages; say 10 paragraphs)
Will need to break down into background research topics. Need to clarify how throughout each topic should be. Should be OK. 10 Paragraphs is not a lot.

Project Description: (5 pages; say 12 paragraphs including 2-3 figure).
There's a lot of space to write about the actual project. I'm not clear why. Assuming the project is not supposed to be implemented this needs to be clarified, but will probably initially go into details on the actual collection (“field work”) as well as the data extraction. Possibly 3 pages.
Then specify over data analysis.
This section requires further (major) thought and planning.

Budget: (1 page)
Again, “field work” will likely be considered within the extent of the project. I see no way around it unless I'm missing something. Shouldn't be a problem though.

Conclusions: (2 pages)
should relate policy to the world of ecology. Should be interesting enough

This should be step I alongside the introduction, to review literature.

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The microbial genetic composite of surface freshwater communities and water salinity in the upper Mississippi river: a case study for using metagenomics for monitoring water content and quality in lotic freshwater ecosystems

Freshwater ecosystems are a subset of Earth's aquatic ecosystems which includes lakes and ponds, rivers, streams, springs, and wetlands. According to a study by Vörösmarty et al. (2010) high quality freshwater is an essential natural resource which is increasingly threatened by global changes. The study found that 65% of global river discharge and the aquatic habitat supported by this water is under moderate to high threat, and that freshwater diversity may be in a state of crisis. While ground water is protected by the overlying strata and the sea can disperse pollutants, lotic ecosystems (streams or rivers) are highly vulnerable to activities at its basin. The group was unable to compute a globally meaningful estimate of adjusted biodiversity threat due to the “paucity of relevant data”. In the past hydrologists found it similarly difficult coping with water quality problems. The importance and breadth of effort put forward to address the topic is best illustrated by the fact that 12 USA federal agencies and more than 100 non-federal groups now take part in administrating water quality standards, irrespective of global bodies such as UNESCO and the World Health Organization.
Water bodies can be fully characterized by three major components: hydrology, physico-chemistry, and biology. To that end, water quality assessment is the overall process of evaluation these components, and water quality monitoring is a standardized collection of relevant information. While monitoring of water quality is a key element in current day to day environmental and sanitary engineering, notwithstanding, an ongoing research effort is paramount in improving and expanding on the ability to assess water quality and set standards, so as to identify both local and global trends in the change of water quality. While original efforts to understand and monitor freshwater ecosystems were spurred on by threats to human health such as Cholera, in the past decades biologists have also been studying the effects of human activities on the biology of aquatic systems, and their recent findings are increasingly being translated into new methods for systematically monitoring the quality of water bodies in new ways. Amongst the approaches and methods for monitoring by the use of bioindicating organisms are Physiological and biochemical methods test for metabolic activity or biochemical effects. Ecological methods test for the absence of organisms or changes in the structure a community, and histological and morphological methods test for changes in the morphology of an organisms. Under more scrupulous monitoring or a survey, organisms may be physically controlled for contaminants – whether by sampling in situ or by a controlled experiment. Specifically, monitoring of lotic freshwater often involves relating conditions through groups of...

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