## 1 Introduction  
Lake eutrophication has become one of the most serious ecological problems of the 21 st century [1]. In aquatic ecosystems, especially for shallow lakes, eutrophication is often caused by excessive nutrient loading (i.e., N and P) [2, 3]. Eutrophication is often accompanied by undesirable overgrowth of autotrophs, such as cyanobacteria and algae, which form a greenish slime layer on the surface of lake water and restrict light penetration [4]. Eutrophication also triggers instability of the ecosystems, which can easily be invaded by aquatic plants. Eutrophication can create enough nutrients for aquatic plant growth. Therefore, macrophtyes usually spread rapidly in these shallow water areas, which include wetlands, fens, and peat lakes [5, 6]. In some lakes, restoration of macrophtyes has been proposed as an ecological strategy to improve water quality and to rehabilitate the degraded lake ecosystem, which also causes rapid aquatic plant growth [7]. Once decayed, plant tissues become abundant and settle into sediments as litter.  
Decomposition of excess litter may generate a series of negative influences on lake ecosystems. First, because the refractory lignocellulosic is the major component of plants, decomposition of plant litter causes an increase in sediment layer, reducing lake area, damaging animal habitats, and accelerating lake swamping [8]. Second, the accumulation and decomposition of dead litter consume oxygen and generate greenhouse gases such as hydrogen sulfide (H\({}_{2}\)S) and methane (CH\({}_{4}\)) [9]. Once that happens, many fish species and macroinvertebrates can suffocate and die, while species that live at the bottom of such lakes can die off completely [10].  
In sediments, the removal of lignocellulosic is mostly mediated by microbial extracellular enzymes [11]. In fact, the biodegradation rate of plant litter in sediments is low and is usually due to the lack of suitable and adequate electron acceptors, such as oxygen, ferric iron, nitrate, and sulfate. Therefore, a complementary technique to effectively remove and obtain energy from lignocellulosic is needed. Recent studies have shown that the anode of sediment microbial fuel cell (SMFC) can act as an effective electron acceptor [12; 13]. SMFC technology can remove organic matter from sediment and provide a low-cost and long-term sink for electrons [14].  
For a typical microbial fuel cell (MFC), organic matter is converted into electricity via the action of bacteria in an anode [15]. SMFCs are the main type of MFCs. They place an anode into organic rich sediment and a cathode on the surface of lake water. Electrons are released during substrate oxidation; then, they are transferred to an anode via anode-respiring bacteria. The anode serves as the electron acceptor. Subsequently, electrons are transported across a load to the cathode and a current is generated when oxygen is reduced in the water column [16]. Our previous research determined that SMFC can speed up the removal of plant litter [17], but it was still unknown whether this removal was influenced by different sources of sediment.  
The overall objectives of this study were to investigate the effects of SMFC on litter removal and how that removal affects the different properties of sediments. During the 700 days of _ex-situ_ pilot-scale lab experiments, sediment samples were extracted from a macrophyte-dominated area and an algae-dominated area in two bays of the shallow eutrophic lake-Taihu lake. The alteration of the organic matter in each of the two sampling sites was characterized and compared. Meanwhile, the composition of microbial communities was identified using high-throughput pyrosequencing technology after 700 days of incubation.