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Photoautotrophic bacteria
The bacterial photoautotroph community of salt marshes primarily consists of cyanobacteria, purple bacteria, and green sulfur bacteria.

Cyanobacteria in salt marshes
Cyanobacteria are important nitrogen fixers in salt marshes, and provide nitrogen to organisms like diatoms and microalgae.

Purple bacteria
Oxygen inhibits photosynthesis in purple bacteria, which makes estuaries a favorable habitat for them due to the low oxygen content and high levels of light present, optimizing their photosynthesis. In anoxic environments, like salt marshes, many microbes have to use sulfate as an electron acceptor during cellular respiration instead of oxygen, producing lots of hydrogen sulfide as a byproduct. While hydrogen sulfide is toxic to most organisms, purple bacteria require it to grow and will metabolize it to either sulfate or sulfur, and by doing so allowing other organisms to inhabit the toxic environment. Purple bacteria can be further classified as either purple sulphur bacteria, or purple non-sulfur bacteria. Purple sulphur bacteria are more tolerant to sulfide and store the sulfur they create intracellularly, while purple non-sulfur bacteria excrete any sulfur they produce.

Green bacteria
Green sulfur bacteria (Chlorobiaceae) are photoautotrophic bacteria that utilize sulfide and thiosulfate for their growth, producing sulfate in the process. They are very adapted to photosynthesizing in low light environments with bacteriochlorophyll pigments a, c, d, and e, to help them absorb wavelengths of light that other organisms cannot. When co-existing with purple bacteria, they often occupy lower depths as they are less tolerant to oxygen, but more photosynthetically adept.

Fungi
Some mycorrhizal fungi, like Arbuscular mycorrhiza are widely associated with salt marsh plants and may even help plants grow in salt marsh soil rich in heavy metals by reducing their uptake into the plant, although the exact mechanism has yet to be determined.

Bacteria
Examining 16S ribosomal DNA found in Yangtze River Estuary, the most common bacteria in the rhizosphere were Proteobacteria such as Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria. One such widespread species had a similar ribotype to the animal pathogen S. marcescens, and may be beneficial for plants as the bacteria can break down chitin into available carbon and nitrogen for plants to use. Actinobacteria have also been found in plant rhizosphere in costal salt marshes and help plants grow through helping plants absorb more nutrients and secreting antimicrobial compounds. In Jiangsu, China, Actinobacteria from the suborders Pseudonocardineae, Corynebacterineae, Propionibacterineae, Streptomycineae, Micromonosporineae, Streptosporangineae and Micrococcineae were cultured and isolated from rhizosphere soil.