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Planctomycetes are classified into two orders: Planctomycetales and Brocadiales. Both are gram-negative bacteria exhibiting unique morphological features. These orders represent distinct lineages within the phylum, with Brocadiales notably containing species capable of anaerobic ammonia oxidation, a specialized metabolic process.

Planctomycetes divide by budding rather than binary fission typical of most bacteria. Motile swarmer cells attach to a surface and develop a stalk at the attachment site. A new cell forms at the opposite pole, develops a flagellum, detaches from the mother cell, and initiates a new cycle, making this reproductive strategy distinctly different from other bacterial phyla.

Pirellulosomes are specialized non-unit membrane-enclosed compartments found in Planctomycetes that contain the nucleoid, ribosomes, and other cytoplasmic components. This compartmentalization resembles eukaryotic organelles, challenging the traditional distinction between prokaryotic and eukaryotic cellular organization. Despite this structural complexity, the DNA remains in a typical bacterial supercoiled state.

The anammoxosome is a specialized compartment found in Brocadiales members like Brocadia anammoxidans that facilitates anaerobic oxidation of ammonia, a form of chemolithoautotrophy. Its unique lipid membrane contains toxic hydrazine intermediates produced during this reaction, protecting cytoplasmic components from damage while enabling this specialized energy-generating process.

In the genus Gemmata, the nucleoid is further enclosed by invaginations of the cell membrane, forming a structure surrounded by a true unit membrane. This creates an additional layer of compartmentalization beyond the pirellulosome found in other Planctomycetes. Despite this membrane-bound organization, the DNA remains in a covalently closed, circular, and supercoiled state characteristic of bacterial genomes.

Planctomycetes possess stalks composed of protein without cell wall or cytoplasm, functioning primarily as attachment mechanisms to surfaces. These stalks are more slender than the prosthecal stalks of related bacteria like Caulobacter. The stalk enables the organism to attach during the budding process and facilitates the development of new cells at the opposite pole.

Planctomycetes exhibit several distinctive surface features including an S-layer in their cell envelope, which is relatively uncommon among bacteria. Many species form rosette-like cell arrangements and possess stalks or appendages. Some species also display filamentous, gliding morphologies, such as Isosphaera found in hot springs, contributing to their morphological distinctiveness within bacterial diversity.